From 12d3da0fdc156279bdce3d7a16e01d66a63626ae Mon Sep 17 00:00:00 2001 From: Xiaohua Zhang Date: Fri, 4 May 2018 16:54:12 -0700 Subject: [PATCH] Add the workflow setting info to README --- README.md | 174 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 174 insertions(+) diff --git a/README.md b/README.md index d1e2f03..eafe3e1 100755 --- a/README.md +++ b/README.md @@ -308,3 +308,177 @@ The "pretty" version the MM/GBSA output ``` +## 3 Work with Maestro workflow + +The following set up works on Cab/Syrah. For other machines, change the commands accordingly. + +### 3.1 Set up python virtual environment + +``` + use -l python + use python-2.7.10 + which pip + pip install --user virtualenv + pip install --user -U virtualenv + pip install --user virtualenvwrapper + export WORKON_HOME=~/.venvs + pip list + pip show virtualenvwrapper + source /g/g92/zhang30/.local/bin/virtualenvwrapper.sh + echo $WORKON_HOME +``` + +put the following two command into your .bashrc or .cshrc + +``` + export WORKON_HOME=~/.venvs + source /g/g92/zhang30/.local/bin/virtualenvwrapper.sh +``` + +### 3.2 Create a virtual environment for conveyorLC + +``` + mkvirtualenv conveyorlc +``` + +### 3.3 Install maestro workflow + +``` + git clone git@github.com:LLNL/maestrowf.git + cd maestrowf/ + git fetch --all + git checkout -t origin/bugfix/dependency_ordering + pip install -e . +``` + +### 3.4 Run the workflow to lauch the conveyorlc pipeline + +``` + workon conveyorlc + mv run_converyorlc.yaml ~/W/ConveyorLC/workflow + cd ~/W/ConveyorLC/workflow + maestro run -h + maestro run ./run_converyorlc.yaml + +``` + +The "maestro run" will crearte a subdirectory using time stamp (i.e. run_converyorlc_20180504-155630) +To check the job status, run "maestro status" + +``` +(conveyorlc)[zhang30@syrah256 workflow]$ maestro status run_converyorlc_20180504-155630 + +Step Name Workspace State Run Time Elapsed Time Start Time Submit Time End Time Number Restarts +------------ ------------------------------- ----------------- -------------- -------------- -------------------------- -------------------------- -------------------------- ----------------- +PPL4parseXML run_converyorlc_20180504-155630 State.INITIALIZED --:--:-- --:--:-- -- -- -- 0 +PPL1Receptor run_converyorlc_20180504-155630 State.FINISHED 0:12:01.079873 0:13:01.157428 2018-05-04 15:57:36.256237 2018-05-04 15:56:36.178682 2018-05-04 16:09:37.336110 0 +PPL4mmgbsa run_converyorlc_20180504-155630 State.RUNNING --:--:-- 0:30:03.091956 2018-05-04 16:12:37.699076 2018-05-04 16:11:37.603008 -- 0 +PPL2Ligand run_converyorlc_20180504-155630 State.FINISHED 0:01:00.053917 0:02:00.187536 2018-05-04 15:57:36.256309 2018-05-04 15:56:36.122690 2018-05-04 15:58:36.310226 0 +PPL3Docking run_converyorlc_20180504-155630 State.FINISHED 0:01:00.096606 0:02:00.202646 2018-05-04 16:10:37.473674 2018-05-04 16:09:37.367634 2018-05-04 16:11:37.570280 0 +``` + +All the results are under the run_converyorlc_20180504-155630 subdirectory. + + +### 3.4 run_converyorlc.yaml sample file + +``` +description: + name: run_converyorlc + description: | + Run the conveyorlc code. + +env: + variables: + OUTPUT_PATH: ./ + + labels: + SETUP_MAIN: | + export LBindData=$(CONVERYOR_BIN)/data + export PATH=$(CONVERYOR_BIN)/bin:$(BIN_HOME)/bin:$PATH + export AMBERHOME=$(BIN_HOME)/amber10 + export PATH=$AMBERHOME/bin/:$PATH + export INPUTDIR=$(INPUT_DIR) + + dependencies: + paths: + - name: BIN_HOME + path: /usr/gapps/aha/cab + + - name: CONVERYOR_BIN + path: /usr/gapps/aha/cab/conveyorlc_test + + - name: INPUT_DIR + path: /g/g92/zhang30/W/ConveyorLC/workflow + +batch: + type: slurm + host: syrah + bank: bbs + queue: pdebug + +study: + - name: PPL1Receptor + description: Run Lingand preparation step of the pipeline. + run: + cmd: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 3p] PPL1Receptor --input $(INPUT_DIR)/pdb.list --output out + restart: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 3p] PPL1Receptor --input $(INPUT_DIR)/pdb.list --output out + walltime: "00:30:00" + nodes: 1 + procs: 3 + + - name: PPL2Ligand + description: Run Lingand preparation step of the pipeline. + run: + cmd: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 16p] PPL2Ligand --sdf $(INPUT_DIR)/pur2.sdf + restart: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 16p] PPL2Ligand --sdf $(INPUT_DIR)/pur2.sdf + walltime: "00:30:00" + nodes: 1 + procs: 16 + + - name: PPL3Docking + description: Run docking calculations. + run: + cmd: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 4p] PPL3Docking --recXML PPL1Track.xml --ligXML PPL2Track.xml --exhaustiveness 2 --num_modes 1 + restart: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 4p] PPL3Docking --recXML PPL1Track.xml --ligXML PPL2Track.xml --exhaustiveness 2 --num_modes 1 + depends: [PPL1Receptor, PPL2Ligand] + walltime: "00:30:00" + nodes: 1 + procs: 4 + cores per task: 4 + + - name: PPL4mmgbsa + description: Run docking calculations. + run: + cmd: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 16p] PPL4mmgbsa --comXML PPL3Track.xml + restart: | + $(SETUP_MAIN) + $(LAUNCHER)[1n, 16p] PPL4mmgbsa --comXML PPL3Track.xml + depends: [PPL3Docking] + walltime: "00:30:00" + nodes: 1 + procs: 16 + + - name: PPL4parseXML + description: Convert PPL4Track.xml to readable XML file. + run: + cmd: | + $(SETUP_MAIN) + PPL4parseXML --inXML PPL4TrackTemp.xml --outXML PPL4Parse.xml + depends: [PPL4mmgbsa] +``` +