Merge pull request #4 from modl-uclouvain/tuto_part1

Tuto part1

.gitignore

+
 # mongodb instance folder
 db/
 
@@ -5,6 +6,9 @@ db/
 tutorials/flow_sic_relax
 tutorials/launcher_*/
 
+# VSCode IDE
+.vscode
+
 # https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
 # General
 .DS_Store

Dockerfile

@@ -24,7 +24,7 @@ RUN apt-get update \
 WORKDIR /tmp
 
 ARG abinit_version="9.4.0"
-COPY configs/abinit_config.ac9 /tmp/abinit-${abinit_version}/build/abinit_config.ac9
+COPY configs/abinit/abinit_config.ac9 /tmp/abinit-${abinit_version}/build/abinit_config.ac9
 
 RUN wget -k "https://www.abinit.org/sites/default/files/packages/abinit-${abinit_version}.tar.gz" \
  && tar xzf abinit-${abinit_version}.tar.gz \
@@ -38,11 +38,34 @@ RUN wget -k "https://www.abinit.org/sites/default/files/packages/abinit-${abinit
 FROM jupyter/scipy-notebook
 LABEL maintainer="Gian-Marco Rignanese <gian-marco.rignanese@uclouvain.be>"
 
+
+# Setup slurm
+# ===========
+
+USER root
+
+RUN apt-get update \
+ && apt install -y --no-install-recommends \
+    slurmd slurm-client slurmctld \
+ && rm -rf /var/lib/apt/lists/*
+
+COPY configs/slurm/slurm.conf /etc/slurm-llnl/slurm.conf
+COPY configs/slurm/start_slurm.sh  /usr/local/bin/before-notebook.d/
+
+# https://github.com/yuwata/slurm-fedora/blob/master/slurm-setuser.in
+RUN mkdir -p /run/munge \
+ && chown -R jovyan /run/munge /etc/munge /var/lib/munge /var/log/munge \
+ && mkdir -p /var/run/slurm-llnl \
+ && chown -R jovyan /var/run/slurm-llnl /var/lib/slurm-llnl /var/log/slurm-llnl
+
+USER $NB_UID
+
+
 # Abinit installation
 # ===================
-# # 1. MPI libraries - choice for Open MPI: mpi-default-bin openmpi-bin libopenmpi3
-# # 2. math libraries - choice for lapack and blas: liblapack3 libblas3
-# # 3. mandatory libraries: libhdf5-103 libnetcdf15 libnetcdff7 libpnetcdf0d libxc5 libfftw3-bin libxml2
+# - MPI libraries - choice for Open MPI: mpi-default-bin openmpi-bin libopenmpi3
+# - math libraries - choice for lapack and blas: liblapack3 libblas3
+# - mandatory libraries: libhdf5-103 libnetcdf15 libnetcdff7 libpnetcdf0d libxc5 libfftw3-bin libxml2
 
 USER root
 
@@ -62,46 +85,34 @@ ENV PATH=/opt/abinit/bin:$PATH
 
 # Install Python 3 packages
 # =========================
-# fireworks's depenecies: flask-paginate gunicorn pymongo
-# pseudo_dojo's depenecies: periodic-table-plotter atomicfile
+# Depenecies:
+# - fireworks: flask-paginate gunicorn pymongo
+# - pseudo_dojo: periodic-table-plotter atomicfile
 
 RUN conda install --quiet --yes \
     'abipy' \
     'jupyter-server-proxy' \
     'flask-paginate' 'gunicorn' 'pymongo' \
     'periodic-table-plotter' 'atomicfile' \
- && pip install --no-cache-dir jupyter-jsmol fireworks \
+ && pip install --no-cache-dir jupyter-jsmol \
+ && pip install --no-cache-dir git+https://github.com/modl-uclouvain/fireworks.git \
+ && pip install --no-cache-dir jupyter-fireworks-proxy \
+ && pip install --no-cache-dir git+https://github.com/gpetretto/abiflows.git@develop \
  && conda clean --all -f -y \
  && fix-permissions "${CONDA_DIR}" \
  && fix-permissions "/home/${NB_USER}"
 
-# Pseudo-dojo
-# ===========
-
+# Install a "lightweight" version of Pseudo-dojo
 COPY --chown=$NB_UID:$NB_GID pseudo_dojo /opt/pseudo_dojo
 WORKDIR /opt/pseudo_dojo
 RUN pip install -e .
 
-# Setup slurm
-# ===========
-
-USER root
-
-RUN apt-get update \
- && apt install -y --no-install-recommends \
-    slurmd slurm-client slurmctld \
- && rm -rf /var/lib/apt/lists/*
-
-COPY configs/slurm.conf /etc/slurm-llnl/slurm.conf
-COPY configs/start_slurm.sh  /usr/local/bin/before-notebook.d/
-
-# https://github.com/yuwata/slurm-fedora/blob/master/slurm-setuser.in
-RUN mkdir -p /run/munge \
- && chown -R jovyan /run/munge /etc/munge /var/lib/munge /var/log/munge \
- && mkdir -p /var/run/slurm-llnl \
- && chown -R jovyan /var/run/slurm-llnl /var/lib/slurm-llnl /var/log/slurm-llnl
+# Setup home folder 
+# =================
 
-USER $NB_UID
 WORKDIR $HOME
 
+COPY --chown=$NB_UID:$NB_GID configs/abipy .abinit/abipy
+COPY --chown=$NB_UID:$NB_GID configs/fireworks .fireworks
+
 COPY --chown=$NB_UID:$NB_GID tutorials tutorials

configs/abipy/fw_manager.yaml

+fw_policy:
+    autoparal: True
+    rerun_same_dir: False
+    allow_local_restart: False
+    mpirun_cmd: mpirun
+    max_restarts: 30
+    abipy_manager: /home/jovyan/.abinit/abipy/manager.yml
+

configs/abipy/manager.yml

+
+## Local runner ##############
+
+# policy:
+#   autoparal: 0
+
+hardware: &hardware
+  num_nodes: 1
+  sockets_per_node: 1
+  cores_per_socket: 4
+  mem_per_node: 16 Gb
+
+job: &job
+  mpi_runner: "mpirun"
+  # pre_run: "export PATH=$HOME/git_repos/abinit/build_gcc/src/98_main:$PATH"
+
+
+qadapters: # List of `qadapters` objects  (just one in this simplified example)
+  - priority: 2
+    queue:
+      qtype: shell        # "Submit" jobs via the shell.
+      qname: localhost    # "Submit" to the localhost queue
+                        # (it's a fake queue in this case)
+
+    limits:
+      timelimit: 01:00:00   #  Time-limit for each task.
+      max_cores: 4          #  Max number of cores that can be used by a single task.
+      hint_cores:  2
+
+    hardware: *hardware
+    job: *job
+
+
+  - priority: 1
+    queue:
+      qname: debug
+      qtype: slurm
+    limits:
+      timelimit: 2:00:0
+      min_cores: 1
+      max_cores: 2
+      min_mem_per_proc: 1
+    hardware: *hardware
+    job: *job
+
+
+##############################

configs/fireworks/FW_config.yaml

+PRINT_FW_JSON: True
+LAUNCHPAD_LOC: /home/jovyan/.fireworks/my_launchpad.yaml
+FWORKER_LOC: /home/jovyan/.fireworks/my_fworker.yaml
+QUEUEADAPTER_LOC: /home/jovyan/.fireworks/my_qadapter.yaml
+SUBMIT_SCRIPT_NAME: FW_submit.script
+QUEUE_UPDATE_INTERVAL: 3
+EXCEPT_DETAILS_ON_RERUN: True
+REMOVE_USELESS_DIRS: True

configs/fireworks/SLURM_template.txt

+#!/bin/bash -l
+
+#SBATCH --nodes=$${nodes}
+#SBATCH --ntasks=$${ntasks}
+#SBATCH --ntasks-per-node=$${ntasks_per_node}
+#SBATCH --ntasks-per-core=$${ntasks_per_core}
+#SBATCH --core-spec=$${core_spec}
+#SBATCH --exclude=$${exclude_nodes}
+#SBATCH --cpus-per-task=$${cpus_per_task}
+#SBATCH --gpus-per-task=$${gpus_per_task}
+#SBATCH --gres=$${gres}
+#SBATCH --qos=$${qos}
+#SBATCH --time=$${walltime}
+#SBATCH --time-min=$${time_min}
+#SBATCH --partition=$${queue}
+#SBATCH --account=$${account}
+#SBATCH --job-name=$${job_name}
+#SBATCH --license=$${license}
+#SBATCH --output=$${job_name}-%j.out
+#SBATCH --error=$${job_name}-%j.error
+#SBATCH --constraint=$${constraint}
+#SBATCH --signal=$${signal}
+#SBATCH --mem=$${mem}
+#SBATCH --mem-per-cpu=$${mem_per_cpu}
+#SBATCH --mail-type=$${mail_type}
+#SBATCH --mail-user=$${mail_user}
+
+
+$${pre_rocket}
+cd $${launch_dir}
+$${rocket_launch}
+$${post_rocket}
+

configs/fireworks/my_fworker.yaml

+name: jovyan_worker
+category: ''
+query: '{}'

configs/fireworks/my_qadapter.yaml

+_fw_name: CommonAdapter
+_fw_q_type: SLURM
+_fw_template_file: /home/jovyan/.fireworks/SLURM_template.txt
+rocket_launch: rlaunch singleshot
+ntasks: 1
+walltime: '02:0:0'
+queue: debug
+account: null
+job_name: null
+pre_rocket: null
+post_rocket: null

configs/slurm.conf → configs/slurm/slurm.conf

@@ -45,5 +45,5 @@ SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log
 SlurmdLogFile=/var/log/slurm-llnl/slurmd.log
 
 # COMPUTE NODES
-NodeName=localhost CPUs=1 State=UNKNOWN
+NodeName=localhost CPUs=4 State=UNKNOWN
 PartitionName=debug Nodes=localhost Default=YES MaxTime=INFINITE State=UP

docker-compose.dev.yml

+version: '3.1'
+services:
+
+  workflows-workshop:
+    # build: .
+    image: workflows-workshop:latest
+    restart: always
+    user: root
+    environment:
+      # - NB_UID=1001
+      - GRANT_SUDO=yes
+      - OMPI_MCA_btl_vader_single_copy_mechanism=none
+    ports:
+      - 8888:8888
+      - 5000:5000
+    depends_on:
+      - mongo
+    volumes:
+      - ./tutorials:/home/jovyan/tutorials
+
+  mongo:
+    image: mongo
+    restart: always
+    # environment:
+    #   - MONGO_INITDB_ROOT_USERNAME=admin
+    #   - MONGO_INITDB_ROOT_PASSWORD=secret
+    # ports:
+    #   - 27017:27017  # opening port for development only!
+    volumes:
+      - ./db:/data/db
+
+  # mongo-express:  # mongo-express only for development only!
+  #   image: mongo-express
+  #   restart: always
+  #   ports:
+  #     - 8081:8081
+  #   environment:
+  #     - ME_CONFIG_MONGODB_ADMINUSERNAME=admin
+  #     - ME_CONFIG_MONGODB_ADMINPASSWORD=secret
+  #   depends_on:
+  #     - mongo

docker-compose.yml

@@ -2,39 +2,15 @@ version: '3.1'
 services:
 
   workflows-workshop:
-    # build: .
     image: workflows-workshop:latest
     restart: always
-    user: root
     environment:
-      # - NB_UID=1001
-      - GRANT_SUDO=yes
+      - OMPI_MCA_btl_vader_single_copy_mechanism=none
     ports:
       - 8888:8888
-      - 5000:5000
     depends_on:
       - mongo
-    volumes:
-      - ./tutorials:/home/jovyan/tutorials
-
+  
   mongo:
     image: mongo
     restart: always
-    # environment:
-    #   - MONGO_INITDB_ROOT_USERNAME=admin
-    #   - MONGO_INITDB_ROOT_PASSWORD=secret
-    # ports:
-    #   - 27017:27017  # opening port for development only!
-    volumes:
-      - ./db:/data/db
-
-  # mongo-express:  # mongo-express only for development only!
-  #   image: mongo-express
-  #   restart: always
-  #   ports:
-  #     - 8081:8081
-  #   environment:
-  #     - ME_CONFIG_MONGODB_ADMINUSERNAME=admin
-  #     - ME_CONFIG_MONGODB_ADMINPASSWORD=secret
-  #   depends_on:
-  #     - mongo

tutorials/Abinit - quickstart.ipynb

-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "exempt-cloud",
-   "metadata": {},
-   "source": [
-    "# Abinit - quickstart\n",
-    "\n",
-    "https://abinit.github.io/abipy/flow_gallery/run_sic_relax.html#sphx-glr-flow-gallery-run-sic-relax-py"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "necessary-budapest",
-   "metadata": {
-    "scrolled": false
-   },
-   "outputs": [],
-   "source": [
-    "!abicheck.py"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "chronic-invention",
-   "metadata": {},
-   "source": [
-    "## Relaxation Flow\n",
-    "\n",
-    "This example shows how to build a very simple Flow for the structural relaxation of SiC. One could use a similar logic to perform multiple relaxations with different input parameters…\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "handmade-dividend",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import abipy.abilab as abilab\n",
-    "import abipy.data as data\n",
-    "import abipy.flowtk as flowtk\n",
-    "\n",
-    "\n",
-    "def build_flow(workdir):\n",
-    "\n",
-    "    pseudos = data.pseudos(\"14si.pspnc\", \"6c.pspnc\")\n",
-    "    structure = data.structure_from_ucell(\"SiC\")\n",
-    "\n",
-    "    # Initialize the input\n",
-    "    relax_inp = abilab.AbinitInput(structure, pseudos=pseudos)\n",
-    "\n",
-    "    # Set variables\n",
-    "    relax_inp.set_vars(\n",
-    "        ecut=20,\n",
-    "        paral_kgb=1,\n",
-    "        iomode=3,\n",
-    "        # Relaxation part\n",
-    "        ionmov=2,\n",
-    "        optcell=1,\n",
-    "        strfact=100,\n",
-    "        ecutsm=0.5,       # Important!\n",
-    "        dilatmx=1.15,     # Important!\n",
-    "        toldff=1e-6,\n",
-    "        tolmxf=1e-5,\n",
-    "        ntime=100,\n",
-    "    )\n",
-    "\n",
-    "    # K-points sampling\n",
-    "    shiftk = [\n",
-    "        [0.5,0.5,0.5],\n",
-    "        [0.5,0.0,0.0],\n",
-    "        [0.0,0.5,0.0],\n",
-    "        [0.0,0.0,0.5]\n",
-    "    ]\n",
-    "    relax_inp.set_kmesh(ngkpt=[4, 4, 4], shiftk=shiftk)\n",
-    "\n",
-    "    # Initialize the flow\n",
-    "    flow = flowtk.Flow(workdir)\n",
-    "\n",
-    "    # Register the task.\n",
-    "    flow.register_relax_task(relax_inp)\n",
-    "\n",
-    "    return flow"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "related-music",
-   "metadata": {},
-   "source": [
-    "Build and run the flow:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "steady-fellowship",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "flow = build_flow('flow_sic_relax')\n",
-    "flow.rmtree()\n",
-    "\n",
-    "scheduler = flow.make_scheduler()\n",
-    "scheduler.start()\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "confirmed-space",
-   "metadata": {},
-   "source": [
-    "To visualize the evolution of the lattice parameters during the structura relaxation use:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "raising-valuable",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "abifile = abilab.abiopen('flow_sic_relax/w0/t0/outdata/out_HIST.nc')\n",
-    "abifile.plot();"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "changing-bennett",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "passing-mineral",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "prescribed-mexico",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

tutorials/manager.yml

-
-## Local runner ##############
-
-# policy:
-#   autoparal: 0
-
-qadapters: # List of `qadapters` objects  (just one in this simplified example)
-- priority: 1
-  queue:
-    qtype: shell        # "Submit" jobs via the shell.
-    qname: localhost    # "Submit" to the localhost queue
-                        # (it's a fake queue in this case)
-
-  job:
-    mpi_runner: "mpirun"
-    # pre_run: "export PATH=$HOME/git_repos/abinit/build_gcc/src/98_main:$PATH"
-
-  limits:
-    timelimit: 01:00:00   #  Time-limit for each task.
-    max_cores: 4          #  Max number of cores that can be used by a single task.
-    hint_cores:  2
-
-  hardware:
-    num_nodes: 1
-    sockets_per_node: 1
-    cores_per_socket: 4
-    mem_per_node: 16 Gb