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Commit ef781e2d authored by muntwiler_m's avatar muntwiler_m
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public release 3.0.0 - see README and CHANGES for details

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.gitlab-ci.yml
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pages:
stage: deploy
script:
- ~/miniconda3/bin/activate pmsco
- make docs
- mv docs/html/ public/
artifacts:
......@@ -10,4 +11,4 @@ pages:
- master
tags:
- doxygen
\ No newline at end of file
CHANGES.md
View file @ ef781e2d
Release 3.0.0 (2021-02-01)
==========================
| Hash | Date | Description |
| ---- | ---- | ----------- |
| 72a9f38 | 2021-02-06 | introduce run file based job scheduling |
| 42e12d8 | 2021-02-05 | compatibility with recent conda and singularity versions |
| caf9f43 | 2021-02-03 | installation: include plantuml.jar |
| 574c88a | 2021-02-01 | docs: replace doxypy by doxypypy |
| a5cb831 | 2021-02-05 | redefine output_file property |
| 49dbb89 | 2021-01-27 | documentation of run file interface |
| 940d9ae | 2021-01-07 | introduce run file interface |
| 6950f98 | 2021-02-05 | set legacy fortran for compatibility with recent compiler |
| 28d8bc9 | 2021-01-27 | graphics: fixed color range for modulation functions |
| 1382508 | 2021-01-16 | cluster: build_element accepts symbol or number |
| 53508b7 | 2021-01-06 | graphics: swarm plot |
| 4a24163 | 2021-01-05 | graphics: genetic chart |
| 99e9782 | 2020-12-23 | periodic table: use common binding energies in condensed matter XPS |
| fdfcf90 | 2020-12-23 | periodic table: reformat bindingenergy.json, add more import/export functions |
| 13cf90f | 2020-12-21 | hbnni: parameters for xpd demo with two domains |
| 680edb4 | 2020-12-21 | documentation: update documentation of optimizers |
| d909469 | 2020-12-18 | doc: update top components diagram (pmsco module is entry point) |
| 574993e | 2020-12-09 | spectrum: add plot cross section function |
Release 2.2.0 (2020-09-04)
==========================
......
README.md
View file @ ef781e2d
......@@ -6,7 +6,7 @@ It is a collection of computer programs to calculate photoelectron diffraction p
and to optimize structural models based on measured data.
The actual scattering calculation is done by code developed by other parties.
PMSCO wraps around that program and facilitates parameter handling, cluster building, structural optimization and parallel processing.
PMSCO wraps around those programs and facilitates parameter handling, cluster building, structural optimization and parallel processing.
In the current version, the [EDAC](http://garciadeabajos-group.icfo.es/widgets/edac/) code
developed by F. J. García de Abajo, M. A. Van Hove, and C. S. Fadley (1999) is used for scattering calculations.
Instead of EDAC built-in routines, alternatively,
......@@ -20,11 +20,12 @@ Highlights
- various scanning modes including energy, manipulator angle (polar/azimuthal), emission angle.
- averaging over multiple domains and emitters.
- global optimization of multiple scans.
- structural optimization algorithms: particle swarm optimization, grid search, gradient search.
- structural optimization algorithms: particle swarm optimization, genetic algorithm, grid scan, table scan.
- detailed reports and graphs of result files.
- calculation of the modulation function.
- calculation of the weighted R-factor.
- automatic parallel processing using OpenMPI.
- tested on Linux cluster machines.
- compatible with Slurm resource manager on Linux cluster machines.
Installation
......@@ -39,13 +40,12 @@ The code requires about 2 GB of RAM per process.
Detailed installation instructions and dependencies can be found in the documentation
(docs/src/installation.dox).
A [Doxygen](http://www.stack.nl/~dimitri/doxygen/index.html) compiler with Doxypy is required to generate the documentation in HTML or LaTeX format.
A [Doxygen](http://www.stack.nl/~dimitri/doxygen/index.html) compiler with Doxypypy is required to generate the documentation in HTML format.
The easiest way to set up an environment with all dependencies and without side-effects on other installed software is to use a [Singularity](https://www.sylabs.io/guides/2.5/user-guide/index.html) container.
A Singularity recipe file is part of the distribution, see the PMSCO documentation for details.
On newer Linux systems (e.g. Ubuntu 18.04), Singularity is available from the package manager.
Installation in a [virtual box](https://www.virtualbox.org/) on Windows or Mac is straightforward using the [Vagrant](https://www.vagrantup.com/) system.
A Vagrant file is included in the distribution.
The easiest way to set up an environment with all dependencies and without side-effects on other installed software is to use a [Singularity](https://www.sylabs.io/guides/3.7/user-guide/index.html) container.
A Singularity recipe file is part of the distribution, see the PMSCO documentation for details, Singularity must be installed separately.
Installation in a [virtual box](https://www.virtualbox.org/) on Windows or Mac is straightforward using pre-compiled images with [Vagrant](https://www.vagrantup.com/).
A Vagrant definition file is included in the distribution.
The public distribution of PMSCO does not contain the [EDAC](http://garciadeabajos-group.icfo.es/widgets/edac/) code.
Please obtain the EDAC source code from the original author, copy it to the pmsco/edac directory, and apply the edac_all.patch patch.
......@@ -70,7 +70,7 @@ Matthias Muntwiler, <mailto:matthias.muntwiler@psi.ch>
Copyright
---------
Copyright 2015-2020 by [Paul Scherrer Institut](http://www.psi.ch)
Copyright 2015-2021 by [Paul Scherrer Institut](http://www.psi.ch)
Release Notes
......@@ -78,6 +78,22 @@ Release Notes
For a detailed list of changes, see the CHANGES.md file.
3.0.0 (2021-02-08)
------------------
- Run file interface replaces command line arguments:
- Specify all run-time parameters in a JSON-formatted text file.
- Override any public attribute of the project class.
- Only the name of the run file is needed on the command line.
- The command line interface is still available, some default values and the handling of directory paths have changed.
Check your code for compatibility.
- Integrated job scheduling with the Slurm resource manager:
- Declare all job arguments in the run file and have PMSCO submit the job.
- Graphics scripts for genetic chart and swarm population (experimental feature).
- Update for compatibility with recent Ubuntu (20.04), Anaconda (4.8) and Singularity (3.7).
- Drop compatibility with Python 2.7, minimum requirement is Python 3.6.
2.2.0 (2020-09-04)
------------------
......
bin/pmsco.ra-git.template deleted 100644 → 0
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#!/bin/bash
#
# Slurm script template for PMSCO calculations on the Ra cluster
# based on run_mpi_HPL_nodes-2.sl by V. Markushin 2016-03-01
#
# this version checks out the source code from a git repository
# to a temporary location and compiles the code.
# this is to minimize conflicts between different jobs
# but requires that each job has its own git commit.
#
# Use:
# - enter the appropriate parameters and save as a new file.
# - call the sbatch command to pass the job script.
# request a specific number of nodes and tasks.
# example:
# sbatch --nodes=2 --ntasks-per-node=24 --time=02:00:00 run_pmsco.sl
# the qpmsco script does all this for you.
#
# PMSCO arguments
# copy this template to a new file, and set the arguments
#
# PMSCO_WORK_DIR
# path to be used as working directory.
# contains the script derived from this template
# and a copy of the pmsco code in the 'pmsco' directory.
# receives output and temporary files.
#
# PMSCO_PROJECT_FILE
# python module that declares the project and starts the calculation.
# must include the file path relative to $PMSCO_WORK_DIR.
#
# PMSCO_OUT
# name of output file. should not include a path.
#
# all paths are relative to $PMSCO_WORK_DIR or (better) absolute.
#
#
# Further arguments
#
# PMSCO_JOBNAME (required)
# the job name is the base name for output files.
#
# PMSCO_WALLTIME_HR (integer, required)
# wall time limit in hours. must be integer, minimum 1.
# this value is passed to PMSCO.
# it should specify the same amount of wall time as requested from the scheduler.
#
# PMSCO_PROJECT_ARGS (optional)
# extra arguments that are parsed by the project module.
#
#SBATCH --job-name="_PMSCO_JOBNAME"
#SBATCH --output="_PMSCO_JOBNAME.o.%j"
#SBATCH --error="_PMSCO_JOBNAME.e.%j"
PMSCO_WORK_DIR="_PMSCO_WORK_DIR"
PMSCO_JOBNAME="_PMSCO_JOBNAME"
PMSCO_WALLTIME_HR=_PMSCO_WALLTIME_HR
PMSCO_PROJECT_FILE="_PMSCO_PROJECT_FILE"
PMSCO_OUT="_PMSCO_JOBNAME"
PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS"
module load psi-python36/4.4.0
module load gcc/4.8.5
module load openmpi/3.1.3
source activate pmsco3
echo '================================================================================'
echo "=== Running $0 at the following time and place:"
date
/bin/hostname
cd $PMSCO_WORK_DIR
pwd
ls -lA
#the intel compiler is currently not compatible with mpi4py. -mm 170131
#echo
#echo '================================================================================'
#echo "=== Setting the environment to use Intel Cluster Studio XE 2016 Update 2 intel/16.2:"
#cmd="source /opt/psi/Programming/intel/16.2/bin/compilervars.sh intel64"
#echo $cmd
#$cmd
echo
echo '================================================================================'
echo "=== The environment is set as following:"
env
echo
echo '================================================================================'
echo "BEGIN test"
which mpirun
cmd="mpirun /bin/hostname"
echo $cmd
$cmd
echo "END test"
echo
echo '================================================================================'
echo "BEGIN mpirun pmsco"
echo
cd "$PMSCO_WORK_DIR"
cd pmsco
echo "code revision"
git log --pretty=tformat:'%h %ai %d' -1
make -C pmsco all
python -m compileall pmsco
python -m compileall projects
echo
cd "$PMSCO_WORK_DIR"
PMSCO_CMD="python pmsco/pmsco $PMSCO_PROJECT_FILE"
PMSCO_ARGS="$PMSCO_PROJECT_ARGS"
if [ -n "$PMSCO_SCAN_FILES" ]; then
PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS"
fi
if [ -n "$PMSCO_OUT" ]; then
PMSCO_ARGS="-o $PMSCO_OUT $PMSCO_ARGS"
fi
if [ "$PMSCO_WALLTIME_HR" -ge 1 ]; then
PMSCO_ARGS="-t $PMSCO_WALLTIME_HR $PMSCO_ARGS"
fi
if [ -n "$PMSCO_LOGLEVEL" ]; then
PMSCO_ARGS="--log-level $PMSCO_LOGLEVEL --log-file $PMSCO_JOBNAME.log $PMSCO_ARGS"
fi
# Do no use the OpenMPI specific options, like "-x LD_LIBRARY_PATH", with the Intel mpirun.
cmd="mpirun $PMSCO_CMD $PMSCO_ARGS"
echo $cmd
$cmd
echo "END mpirun pmsco"
echo '================================================================================'
cd "$PMSCO_WORK_DIR"
rm -rf pmsco
date
ls -lAtr
echo '================================================================================'
exit 0
bin/pmsco.ra.template deleted 100644 → 0
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#!/bin/bash
#
# Slurm script template for PMSCO calculations on the Ra cluster
# based on run_mpi_HPL_nodes-2.sl by V. Markushin 2016-03-01
#
# Use:
# - enter the appropriate parameters and save as a new file.
# - call the sbatch command to pass the job script.
# request a specific number of nodes and tasks.
# example:
# sbatch --nodes=2 --ntasks-per-node=24 --time=02:00:00 run_pmsco.sl
#
# PMSCO arguments
# copy this template to a new file, and set the arguments
#
# PMSCO_WORK_DIR
# path to be used as working directory.
# contains the script derived from this template.
# receives output and temporary files.
#
# PMSCO_PROJECT_FILE
# python module that declares the project and starts the calculation.
# must include the file path relative to $PMSCO_WORK_DIR.
#
# PMSCO_SOURCE_DIR
# path to the pmsco source directory
# (the directory which contains the bin, lib, pmsco sub-directories)
#
# PMSCO_SCAN_FILES
# list of scan files.
#
# PMSCO_OUT
# name of output file. should not include a path.
#
# all paths are relative to $PMSCO_WORK_DIR or (better) absolute.
#
#
# Further arguments
#
# PMSCO_JOBNAME (required)
# the job name is the base name for output files.
#
# PMSCO_WALLTIME_HR (integer, required)
# wall time limit in hours. must be integer, minimum 1.
# this value is passed to PMSCO.
# it should specify the same amount of wall time as requested from the scheduler.
#
# PMSCO_MODE (optional)
# calculation mode: single, swarm, grid, gradient
#
# PMSCO_CODE (optional)
# calculation code: edac, msc, test
#
# PMSCO_LOGLEVEL (optional)
# request log level: DEBUG, INFO, WARNING, ERROR
# create a log file based on the job name.
#
# PMSCO_PROJECT_ARGS (optional)
# extra arguments that are parsed by the project module.
#
#SBATCH --job-name="_PMSCO_JOBNAME"
#SBATCH --output="_PMSCO_JOBNAME.o.%j"
#SBATCH --error="_PMSCO_JOBNAME.e.%j"
PMSCO_WORK_DIR="_PMSCO_WORK_DIR"
PMSCO_JOBNAME="_PMSCO_JOBNAME"
PMSCO_WALLTIME_HR=_PMSCO_WALLTIME_HR
PMSCO_PROJECT_FILE="_PMSCO_PROJECT_FILE"
PMSCO_MODE="_PMSCO_MODE"
PMSCO_CODE="_PMSCO_CODE"
PMSCO_SOURCE_DIR="_PMSCO_SOURCE_DIR"
PMSCO_SCAN_FILES="_PMSCO_SCAN_FILES"
PMSCO_OUT="_PMSCO_JOBNAME"
PMSCO_LOGLEVEL="_PMSCO_LOGLEVEL"
PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS"
module load psi-python36/4.4.0
module load gcc/4.8.5
module load openmpi/3.1.3
source activate pmsco3
echo '================================================================================'
echo "=== Running $0 at the following time and place:"
date
/bin/hostname
cd $PMSCO_WORK_DIR
pwd
ls -lA
#the intel compiler is currently not compatible with mpi4py. -mm 170131
#echo
#echo '================================================================================'
#echo "=== Setting the environment to use Intel Cluster Studio XE 2016 Update 2 intel/16.2:"
#cmd="source /opt/psi/Programming/intel/16.2/bin/compilervars.sh intel64"
#echo $cmd
#$cmd
echo
echo '================================================================================'
echo "=== The environment is set as following:"
env
echo
echo '================================================================================'
echo "BEGIN test"
echo "=== Intel native mpirun will get the number of nodes and the machinefile from Slurm"
which mpirun
cmd="mpirun /bin/hostname"
echo $cmd
$cmd
echo "END test"
echo
echo '================================================================================'
echo "BEGIN mpirun pmsco"
echo "Intel native mpirun will get the number of nodes and the machinefile from Slurm"
echo
echo "code revision"
cd "$PMSCO_SOURCE_DIR"
git log --pretty=tformat:'%h %ai %d' -1
python -m compileall pmsco
python -m compileall projects
cd "$PMSCO_WORK_DIR"
echo
PMSCO_CMD="python $PMSCO_SOURCE_DIR/pmsco $PMSCO_PROJECT_FILE"
PMSCO_ARGS="$PMSCO_PROJECT_ARGS"
if [ -n "$PMSCO_SCAN_FILES" ]; then
PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS"
fi
if [ -n "$PMSCO_CODE" ]; then
PMSCO_ARGS="-c $PMSCO_CODE $PMSCO_ARGS"
fi
if [ -n "$PMSCO_MODE" ]; then
PMSCO_ARGS="-m $PMSCO_MODE $PMSCO_ARGS"
fi
if [ -n "$PMSCO_OUT" ]; then
PMSCO_ARGS="-o $PMSCO_OUT $PMSCO_ARGS"
fi
if [ "$PMSCO_WALLTIME_HR" -ge 1 ]; then
PMSCO_ARGS="-t $PMSCO_WALLTIME_HR $PMSCO_ARGS"
fi
if [ -n "$PMSCO_LOGLEVEL" ]; then
PMSCO_ARGS="--log-level $PMSCO_LOGLEVEL --log-file $PMSCO_JOBNAME.log $PMSCO_ARGS"
fi
which mpirun
ls -l "$PMSCO_SOURCE_DIR"
ls -l "$PMSCO_PROJECT_FILE"
# Do no use the OpenMPI specific options, like "-x LD_LIBRARY_PATH", with the Intel mpirun.
cmd="mpirun $PMSCO_CMD $PMSCO_ARGS"
echo $cmd
$cmd
echo "END mpirun pmsco"
echo '================================================================================'
date
ls -lAtr
echo '================================================================================'
exit 0
bin/pmsco.sge.template deleted 100644 → 0
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#!/bin/bash
#
# SGE script template for MSC calculations
#
# This script uses the tight integration of openmpi-1.4.5-gcc-4.6.3 in SGE
# using the parallel environment (PE) "orte".
# This script must be used only with qsub command - do NOT run it as a stand-alone
# shell script because it will start all processes on the local node.
#
# PhD arguments
# copy this template to a new file, and set the arguments
#
# PHD_WORK_DIR
# path to be used as working directory.
# contains the SGE script derived from this template.
# receives output and temporary files.
#
# PHD_PROJECT_FILE
# python module that declares the project and starts the calculation.
# must include the file path relative to $PHD_WORK_DIR.
#
# PHD_SOURCE_DIR
# path to the pmsco source directory
# (the directory which contains the bin, lib, pmsco sub-directories)
#
# PHD_SCAN_FILES
# list of scan files.
#
# PHD_OUT
# name of output file. should not include a path.
#
# all paths are relative to $PHD_WORK_DIR or (better) absolute.
#
#
# Further arguments
#
# PHD_JOBNAME (required)
# the job name is the base name for output files.
#
# PHD_NODES (required)
# number of computing nodes (processes) to allocate for the job.
#
# PHD_WALLTIME_HR (required)
# wall time limit (hours)
#
# PHD_WALLTIME_MIN (required)
# wall time limit (minutes)
#
# PHD_MODE (optional)
# calculation mode: single, swarm, grid, gradient
#
# PHD_CODE (optional)
# calculation code: edac, msc, test
#
# PHD_LOGLEVEL (optional)
# request log level: DEBUG, INFO, WARNING, ERROR
# create a log file based on the job name.
#
# PHD_PROJECT_ARGS (optional)
# extra arguments that are parsed by the project module.
#
PHD_WORK_DIR="_PHD_WORK_DIR"
PHD_JOBNAME="_PHD_JOBNAME"
PHD_NODES=_PHD_NODES
PHD_WALLTIME_HR=_PHD_WALLTIME_HR
PHD_WALLTIME_MIN=_PHD_WALLTIME_MIN
PHD_PROJECT_FILE="_PHD_PROJECT_FILE"
PHD_MODE="_PHD_MODE"
PHD_CODE="_PHD_CODE"
PHD_SOURCE_DIR="_PHD_SOURCE_DIR"
PHD_SCAN_FILES="_PHD_SCAN_FILES"
PHD_OUT="_PHD_JOBNAME"
PHD_LOGLEVEL="_PHD_LOGLEVEL"
PHD_PROJECT_ARGS="_PHD_PROJECT_ARGS"
# Define your job name, parallel environment with the number of slots, and run time:
#$ -cwd
#$ -N _PHD_JOBNAME.job
#$ -pe orte _PHD_NODES
#$ -l ram=2G
#$ -l s_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:00
#$ -l h_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:30
#$ -V
###################################################
# Fix the SGE environment-handling bug (bash):
source /usr/share/Modules/init/sh
export -n -f module
# Load the environment modules for this job (the order may be important):
module load python/python-2.7.5
module load gcc/gcc-4.6.3
module load mpi/openmpi-1.4.5-gcc-4.6.3
module load blas/blas-20110419-gcc-4.6.3
module load lapack/lapack-3.4.2-gcc-4.6.3
export LD_LIBRARY_PATH=$PHD_SOURCE_DIR/lib/:$LD_LIBRARY_PATH
###################################################
# Set the environment variables:
MPIEXEC=$OPENMPI/bin/mpiexec
# OPENMPI is set by the mpi/openmpi-* module.
export OMP_NUM_THREADS=1
export OMPI_MCA_btl='openib,sm,self'
# export OMPI_MCA_orte_process_binding=core
##############
# BEGIN DEBUG
# Print the SGE environment on master host:
echo "================================================================"
echo "=== SGE job JOB_NAME=$JOB_NAME JOB_ID=$JOB_ID"
echo "================================================================"
echo DATE=`date`
echo HOSTNAME=`hostname`
echo PWD=`pwd`
echo "NSLOTS=$NSLOTS"
echo "PE_HOSTFILE=$PE_HOSTFILE"
cat $PE_HOSTFILE
echo "================================================================"
echo "Running environment:"
env
echo "================================================================"
echo "Loaded environment modules:"
module list 2>&1
echo
# END DEBUG
##############
##############
# Setup
cd "$PHD_SOURCE_DIR"
python -m compileall .
cd "$PHD_WORK_DIR"
ulimit -c 0
###################################################
# The command to run with mpiexec:
CMD="python $PHD_PROJECT_FILE"
ARGS="$PHD_PROJECT_ARGS"
if [ -n "$PHD_SCAN_FILES" ]; then
ARGS="-s $PHD_SCAN_FILES -- $ARGS"
fi
if [ -n "$PHD_CODE" ]; then
ARGS="-c $PHD_CODE $ARGS"
fi
if [ -n "$PHD_MODE" ]; then
ARGS="-m $PHD_MODE $ARGS"
fi
if [ -n "$PHD_OUT" ]; then
ARGS="-o $PHD_OUT $ARGS"
fi
if [ "$PHD_WALLTIME_HR" -ge 1 ]
then
ARGS="-t $PHD_WALLTIME_HR $ARGS"
else
ARGS="-t 0.5 $ARGS"
fi
if [ -n "$PHD_LOGLEVEL" ]; then
ARGS="--log-level $PHD_LOGLEVEL --log-file $PHD_JOBNAME.log $ARGS"
fi
# The MPI command to run:
MPICMD="$MPIEXEC --prefix $OPENMPI -x PATH -x LD_LIBRARY_PATH -x OMP_NUM_THREADS -x OMPI_MCA_btl -np $NSLOTS $CMD $ARGS"
echo "Command to run:"
echo "$MPICMD"
echo
exec $MPICMD
exit 0
bin/qpmsco.ra-git.sh deleted 100755 → 0
View file @ 2b3dbd8b
#!/bin/sh
#
# submission script for PMSCO calculations on the Ra cluster
#
# this version clones the current git repository at HEAD to the work directory.
# thus, version conflicts between jobs are avoided.
#
if [ $# -lt 1 ]; then
echo "Usage: $0 [NOSUB] GIT_TAG DESTDIR JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT [ARGS [ARGS [...]]]"
echo ""
echo " NOSUB (optional): do not submit the script to the queue. default: submit."
echo " GIT_TAG: git tag or branch name of the code. HEAD for current code."
echo " DESTDIR: destination directory. must exist. a sub-dir \$JOBNAME is created."
echo " JOBNAME (text): name of job. use only alphanumeric characters, no spaces."
echo " NODES (integer): number of computing nodes. (1 node = 24 or 32 processors)."
echo " do not specify more than 2."
echo " TASKS_PER_NODE (integer): 1...24, or 32."
echo " 24 or 32 for full-node allocation."
echo " 1...23 for shared node allocation."
echo " WALLTIME:HOURS (integer): requested wall time."
echo " 1...24 for day partition"
echo " 24...192 for week partition"
echo " 1...192 for shared partition"
echo " PROJECT: python module (file path) that declares the project and starts the calculation."
echo " ARGS (optional): any number of further PMSCO or project arguments (except time)."
echo ""
echo "the job script is written to \$DESTDIR/\$JOBNAME which is also the destination of calculation output."
exit 1
fi
# location of the pmsco package is derived from the path of this script
SCRIPTDIR="$(dirname $(readlink -f $0))"
SOURCEDIR="$(readlink -f $SCRIPTDIR/..)"
PMSCO_SOURCE_DIR="$SOURCEDIR"
# read arguments
if [ "$1" == "NOSUB" ]; then
NOSUB="true"
shift
else
NOSUB="false"
fi
if [ "$1" == "HEAD" ]; then
BRANCH_ARG=""