Merge branch 'bugfix' into 'develop'

Bugfix

See merge request west-devel/West!27

.gitlab-ci.yml

@@ -32,7 +32,7 @@ stages:
     - git clone -b $CI_COMMIT_REF_NAME $CI_REPOSITORY_URL West
     - cd West
     - git describe
-    - make conf PYT=python3
+    - make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
     - make all
     - ls ../bin 
     
@@ -47,7 +47,7 @@ stages:
     - ls bin
     - git clone -b $CI_COMMIT_REF_NAME $CI_REPOSITORY_URL West
     - cd West 
-    - make conf PYT=python3
+    - make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
     - make all > /dev/null
     - useradd -m qe
     - cp -r test-suite /home/qe

AUTHORS.md

@@ -11,6 +11,8 @@ The current list of developers, in alphabetical order:
 
 - Sijia Dong (Argonne National Laboratory)
 - Marco Govoni (Argonne National Laboratory and University of Chicago)
+- Lan Huang (Argonne National Laboratory)
+- Yu Jin (University of Chicago)
 - He Ma (University of Chicago)
 - Han Yang (University of Chicago)
 

CHANGELOG.md

 Change Log
 ==========
 
+v4.2.1 (2020/10/19)
+-------------------
+
+- Added support for python 3.8 (--embed)
+- Updated scripts for RCC-Midway and MacOSX
+- Solved bugs in reporting conf layer in Makefile
+- Updated documentation
+
 v4.2.0 (2020/07/03)
 -------------------
 

Doc/installation.rst

@@ -13,7 +13,7 @@ Configure QuantumEspresso by running the ``configure`` script that comes with th
 
    $ git clone -b 'qe-6.1.0' --single-branch --depth 1 https://gitlab.com/QEF/q-e.git QEdir
    $ cd QEdir
-   $ git clone -b 'v4.1.0' --single-branch --depth 1 http://greatfire.uchicago.edu/west-public/West.git West
+   $ git clone -b 'v4.2.1' --single-branch --depth 1 http://greatfire.uchicago.edu/west-public/West.git West
    $ ./configure 
 
 .. note:: 
@@ -26,7 +26,7 @@ It's now time to create the ``pw.x``, ``wstat.x``, ``wfreq.x``, and ``westpp.x``
    $ cd QEdir
    $ make pw
    $ cd QEdir/West
-   $ make conf PYT=python3
+   $ make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
    $ make all
 
 You have succefully installed QuantumEspresso and WEST if you see the executables ``pw.x``, ``wstat.x``, ``wfreq.x``, and ``westpp.x`` created in the QEdir/bin directory.

Doc/installations/macosx.rst

@@ -26,12 +26,13 @@ WEST executables can be compiled using the following script:
 
    export MY_LIB_PATH=/Users/myname/LIBRARIES
 
-   export CPP='cpp-9'
-   export CC='gcc-9'
+   export CPP='cpp-10'
+   export CC='gcc-10'
    export CFLAGS='-m64 -Wall -Wextra'
    export F77='mpif77'
    export FFLAGS='-m64 -fopenmp'
    export FC='mpif90'
+   export MPIF90='mpif90'
    export F90='mpif90'
    export FCFLAGS='-m64 -fopenmp -Wall -fbacktrace -fbounds-check'
    export BLAS_LIBS=${MY_LIB_PATH}/BLAS/libblas.a
@@ -44,7 +45,7 @@ WEST executables can be compiled using the following script:
    make -j 4 pw
    
    cd West
-   make conf PYT=python3
+   make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
    make all
 
 To use the script do: 

Doc/installations/midway.rst

@@ -20,8 +20,8 @@ WEST executables can be compiled using the following script:
    $ cat build_west.sh
    #!/bin/bash
    
-   module load intelmpi/5.1+intel-16.0 mkl/2017.up4 Anaconda3/5.1.0 
-   
+   module load intelmpi/5.1+intel-16.0 mkl/2017.up4 python/cpython-3.8.5 
+  
    export F77=mpiifort
    export CC=mpiicc
    export MPIF90=mpiifort
@@ -34,11 +34,11 @@ WEST executables can be compiled using the following script:
    export LAPACK_LIBS=" "
    export SCALAPACK_LIBS=" -lmkl_scalapack_lp64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -Wl,--end-group"
    
-   ./configure --enable-parallel --with-scalapack --enable-openmp 
-   make -j 6 pw
+   ./configure --enable-openmp=yes --enable-parallel=yes --with-scalapack=intel --with-hdf5=no
+   make -j 2 pw
    
    cd West
-   make conf PYT=python3
+   make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"
    make all
 
 To use the script do: 
@@ -63,7 +63,7 @@ The following is an example executable script `run_west.sh` to run the `wstat.x`
    #SBATCH --ntasks-per-node=28
    #SBATCH --cpus-per-task=1
 
-   module load intelmpi/5.1+intel-16.0 mkl/2017.up4 Anaconda3/5.1.0
+   module load intelmpi/5.1+intel-16.0 mkl/2017.up4 python/cpython-3.8.5
 
    export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
    NTASKS=$(($SLURM_NTASKS_PER_NODE * $SLURM_JOB_NUM_NODES))

Doc/installations/theta.rst

@@ -32,7 +32,7 @@ WEST executables can be compiled using the following script:
    make pw -j 16
 
    cd West
-   make conf PYT=python3
+   make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags`"
    make all 
 
 To use the script do: 

Makefile

@@ -6,7 +6,7 @@ default :
 	@echo "Welcome to WEST!"
 	@echo ' '
 	@echo 'to install WEST, type at the shell prompt:'
-	@echo '  make conf PYT=python-3'
+	@echo '  make conf PYT=python3 PYT_LDFLAGS="`python3-config --ldflags --embed`"'
 	@echo '  make [-j] target'
 	@echo ' '
 	@echo 'where target identifies one or multiple packages'
@@ -31,7 +31,7 @@ conf:
 	@echo " " > west_make.inc
 	@echo WESTDIR=`pwd` >> west_make.inc
 	@echo PYT=${PYT} >> west_make.inc
-	@if [ -z "${PYT_LDFLAGS}" ] ; then echo PYT_LDFLAGS="`${PYT}-config --ldflags`" >> west_make.inc ; else echo PYT_LDFLAGS=${PYT_LDFLAGS} >> west_make.inc ; fi
+	@echo PYT_LDFLAGS=${PYT_LDFLAGS} >> west_make.inc
 	@echo " "
 	@echo "Generated file: west_make.inc"
 	@cat west_make.inc
@@ -92,6 +92,7 @@ report_build_vars \
 pytools_do
 
 wstat: \
+pytools \
 libraries_do \
 modules_do \
 tools_do \

Pytools/.gitignore

+WEST.egg-info/
+dist/
+files.txt

Pytools/read_json.py

+import json
+import sys
+import os.path
+
+def main():
+
+    fname = str(sys.argv[1])
+    key = str(sys.argv[2])
+
+    if os.path.isfile(fname):
+       with open(fname,"r") as file:
+          data = json.load(file)
+    else : 
+       print("Cannot find FILE: ",fname)
+    print(data[key])
+
+if __name__ == "__main__":
+    main()
+

Pytools/setup.py

+from setuptools import setup
+from setuptools import find_packages
+import json
+
+with open('../VERSION.json',"r") as file:
+    data = json.load(file)
+
+setup(name=data["name"],
+      version=data["version"],
+      packages=find_packages(),
+      description='installation script for WEST',
+      url=data["url"],
+      author='Marco Govoni',
+      author_email='mgovoni@anl.gov',
+      license=data["license"],
+      install_requires=[
+          'numpy',
+          'scipy',
+          'matplotlib',
+          'pyyaml',
+          'datetime',
+          'setuptools',
+          'sphinx_rtd_theme'
+      ],
+      python_requires='>=3.6, <4',
+      zip_safe=True)
+

VERSION.json

 {
 "name" : "WEST",
-"version" : "4.2.0",
+"version" : "4.2.1",
 "url" : "http://west-code.org",
 "license" : "GPLv3"
 }