Merge pull request #75 from PrincetonUniversity/ci

Change version to 2.75 and begin to automatically check compilation

.github/workflows/build_use_docker.yml

@@ -0,0 +1,22 @@
+name: build-test
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: zhucaoxiang/stellopt:compile
+    env:
+      MACHINE: docker
+      STELLOPT_PATH: ${{ github.workspace }}
+      OMPI_ALLOW_RUN_AS_ROOT: 1
+      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
+    steps:
+      - name: checkout sources
+        uses: actions/checkout@master
+      - name: compile
+        run: |
+          cd ${STELLOPT_PATH}
+          ./build_all -o clean_debug -j 2
+      - name: test
+        run: |
+          mpiexec ./bin/xstelloptv2 test -h

BENCHMARKS/VMEC_TEST/compare_VMEC.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+@author: Caoxiang Zhu ([email protected])
+For any help, type ./compare_VMEC.py -h
+"""
+import numpy as np
+import xarray
+import argparse
+
+# parse command line arguments
+# =============================================================================
+parser = argparse.ArgumentParser(description="Compare two VMEC netcdf outputs")
+parser.add_argument("filename", type=str, help="file name to be compared")
+parser.add_argument("reference", type=str, help="reference data")
+parser.add_argument("-t", "--tol", type=float, default=1E-8, help="difference tolerance")
+
+args = parser.parse_args()
+print('Compare VMEC outputs in {:s} and {:s} with tolerance {:12.5E}'.format(args.filename, args.reference, args.tol))
+data = xarray.open_dataset(args.filename)
+ref = xarray.open_dataset(args.reference)
+
+tol = args.tol
+match = True
+skip_list = ['version_']
+loose_list = ['jcuru', 'jdotb', 'currumnc', 'currvmnc'] # j related terms must have large tol
+
+print('======================================')
+for key in ref:
+    if key in skip_list:
+        continue
+    if key in loose_list:
+        tol = max(1E-3, tol)
+    else:
+        tol = args.tol
+    try:
+        diff = np.linalg.norm(ref[key].values - data[key].values)/len(ref[key].values)
+        unmatch = diff > tol
+        if unmatch:
+            match = False
+            print('UNMATCHED: '+key+', diff={:12.5E}'.format(diff))
+    except TypeError:
+        pass
+print('  comparison passed: {:} '.format(match))
+print('======================================')
+assert match, 'Differences in some elements are larger than the tolerence.'
+
+exit

BENCHMARKS/makefile

@@ -18,7 +18,7 @@
 
 .PHONY: test_vmec
 
-test_vmec:
+test_vmec: 
 	@echo "Beginning testing of VMEC2000"
 	@cd $(VMEC_TEST_DIR); rm -f jxbout* mercier* threed1* wout*; 
 	@echo $(MPI_RUN) $(MPI_RUN_OPTS_SM) $(MYHOME)/xvmec2000 input.DSHAPE
@@ -45,7 +45,6 @@ test_vmec:
 	@cd $(VMEC_TEST_DIR); $(MPI_RUN) $(MPI_RUN_OPTS_SM) $(MYHOME)/xvmec2000 input.DIII-D
 	@cd $(VMEC_TEST_DIR); ./compare_DIII-D.py
 	@echo "Tesing of VMEC2000 complete"
-	@echo ""
 
 test_diagno:
 	@echo "Beginning testing of DIAGNO"

Dockerfile

@@ -0,0 +1,23 @@
+FROM zhucaoxiang/stellopt:compile
+MAINTAINER Caoxiang Zhu <[email protected]> & STELLOPT developers
+
+WORKDIR /home/STELLOPT
+
+COPY . /home/STELLOPT
+# Compile STELLOPT
+ENV MACHINE="docker"
+ENV STELLOPT_PATH=/home/STELLOPT
+RUN echo $STELLOPT_PATH
+RUN cd $STELLOPT_PATH  && ./build_all -j4 2>&1 | tee log.build 
+RUN chmod -R 777 ${STELLOPT_PATH}/BENCHMARKS
+RUN cp -RP ${STELLOPT_PATH}/bin/* /usr/local/bin/
+
+# add user
+WORKDIR /home/visitor
+RUN groupadd -r visitor -g 433 && \
+useradd -u 431 -r -g visitor -d /home/visitor -s /sbin/nologin -c "Docker image user" visitor && \
+chown -R visitor:visitor /home/visitor
+USER visitor
+
+# Set commands
+CMD ["/bin/bash"]

README.md

@@ -9,38 +9,40 @@ wish to use.  For example to use `SHARE/make_bobdole.inc` you would set
 important to set `STELLOPT_PATH` to the path to your current directory
 where you've pulled the repository.
 
-Once a working copy is developed for your computer, you are welcome 
-to push it back to the main repository for other users.
-Before beginning, it is recommened to create an install branch. To do 
-this issue the following commands from main directory:
+Once you configure the environment variables, you can begin to compile the code by
 
-     git checkout -b install
+     ./build_all 
 
-The -b option tells us to create a new branch (you could also issue
-two commands).  Now you'll be on your install branch feel free to
-edit files as necessary for your installation.  To build the code 
-use the build_all script which will systematically build and compile 
-all the files.
+By default, it will compile all the codes in the folder with the option `clean_release`.
+You can customize the script by providing additional commandline arguments, like `./build_all -o release -j 4 STELLOPTV2`. To check the options, type `./build_all -h`.
 
-For more information, please view [STELLOPT compilation](https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation).
+There is also a Docker image available for use at https://hub.docker.com/r/zhucaoxiang/stellopt.
 
+For more information, please view [STELLOPT compilation](https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation).
 
 # EDITING CODE
-To edit the code please first checkout a new branch with the feature
-you'd like.  Then when you want your changes merged into master,
-please push your branch to the remote:
-
-     git push origin <branchname>
-
+Once a working copy is developed for your computer, you are welcome 
+to push it back to the main repository for other users.
+You can ask for a write permission and push your changes into a remote branch.
 Then submit a pull request through 
 [GitHub](https://github.com/PrincetonUniversity/STELLOPT/pulls).
 
+Or you can share your changes via [git fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo), which doesn't require you have the write permission.
+
+GitHub actions will be triggered by each push and pull-request. The code will be compiled with debug option and you can check the full log at [GitHub actions](https://github.com/PrincetonUniversity/STELLOPT/actions).
 
-# PYTHON INTERFACE
+# UTILITIES
 A Python interface using CTYPES is also included but it requires a
 static shared build of LIBSTELL.  This is still a highly experimental
-option.
+option. You can find the python scripts at `./pySTEL`.
+
+There are also some other plotting packages developed by group members.
+Here are some examples.
+
+  - [matlabVMEC](https://github.com/lazersos/matlabVMEC): MATLAB packages for various codes.
+  - [coilpy](https://github.com/zhucaoxiang/CoilPy): Python package for toroidal Fourier surface, coils, FOCUS and STELLOPT.
 
+If you are willing to share your code, please add your contributions here.
 
 # REPORT BUGS
 If you find any bugs or have any suggestions, please submit an issue 
@@ -54,4 +56,4 @@ You can find some wiki pages at
 [GitHub pages](https://princetonuniversity.github.io/STELLOPT/).
 This is automatically generated from the `markdown` source files 
 in the [gh-pages](https://github.com/PrincetonUniversity/STELLOPT/tree/gh-pages) branch. 
-Everyone is welcome to contribute to the wiki pages.
+You are welcome to report/fix/update the wiki pages.

SHARE/make_docker.inc

@@ -0,0 +1,139 @@
+#######################################################################
+#            Define Basic Utilities
+#######################################################################
+  SHELL = /bin/sh
+  PWD1 = `pwd`
+  MYHOME = $(STELLOPT_PATH)/bin
+  PRECOMP:= /lib/cpp -traditional -DLINUX
+  COMPILE = $(FC)
+  COMPILE_FREE = $(FC) -ffree-form -ffree-line-length-none -ffixed-line-length-none
+  LINK    = ld $(FLAGS) -o
+  LINK_AR = ar -ruv
+  LINK_C  = $(CC) -shared -Wl,-z-defs
+
+#######################################################################
+#            Define Compiler Flags
+#######################################################################
+  FLAGS_R = -O2 -fexternal-blas
+  FLAGS_D = -g -O0 -fexternal-blas -fbacktrace -fcheck=all 
+  LIBS    = -L/usr/lib -lscalapack-openmpi -lblas -llapack
+
+#######################################################################
+#            MPI Options
+#######################################################################
+  LMPI    = T
+  MPI_COMPILE = mpif90
+  MPI_COMPILE_FREE = mpif90 -ffree-form \
+                     -ffree-line-length-none -ffixed-line-length-none
+  MPI_COMPILE_C = mpicc
+  MPI_LINK = mpif90
+  MPI_RUN = mpiexec
+  MPI_RUN_OPTS = 
+#  MPI_RUN_OPTS_SM = -np 16
+#  MPI_RUN_OPTS_MD = -np 64
+#  MPI_RUN_OPTS_LG = -np 256
+
+#######################################################################
+#            NAG Options
+#######################################################################
+  LNAG = F
+  NAG_LIB = -L$(NAG_ROOT)/lib -lnag_nag
+
+#######################################################################
+#            NETCDF Options
+#######################################################################
+  LNETCDF = T
+  NETCDF_INC = -I/usr/include
+  NETCDF_LIB = -L/usr/lib -lnetcdf -lnetcdff
+
+#######################################################################
+#            NTCC Options
+#######################################################################
+  LNTCC = F
+  NTCC_INC = -I/usr/include
+  NTCC_LIB = -L/usr/lib -laladdinsub -lr8slatec -ladpak\
+             -lcppsub -lcomput -lpspline -lportlib -lezcdf -lmds_sub \
+             -lmdstransp -lvaxonly
+
+#######################################################################
+#            HDF5 Options
+#######################################################################
+  LHDF5 = T
+  HDF5_INC = -I/usr/include/hdf5/openmpi
+  HDF5_LIB = -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi \
+             -lhdf5 -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran
+
+#######################################################################
+#             PGPLOT Options
+#######################################################################
+  LPGPLOT = F
+  PGPLOT_INC = -I$(PGPLOT_DIR)
+  PGPLOT_LIB = -L$(PGPLOT_DIR) -lpgplot -L/usr/lib/x86_64-linux-gnu -lX11
+
+#######################################################################
+#             SILO Options
+#######################################################################
+  LSILO = F
+  SILO_INC = -I$(SILOHOME)/include
+  SILO_LIB = -L$(SILOHOME)/lib/x86_64-linux-gnu -lsiloh5
+
+#######################################################################
+#            DKES/NEO Options
+#######################################################################
+  LDKES = T
+  LNEO  = T
+
+#######################################################################
+#            GENE Options
+#######################################################################
+  LGENE = F
+  GENE_INC = -I$(GENE_PATH)
+  GENE_DIR = $(GENE_PATH)
+  LIB_GENE = libgene.a
+  GENE_LIB = $(GENE_DIR)/$(LIB_GENE) \
+             -L/u/slazerso/src/GENE17_2016/external/pppl_cluster/futils/src -lfutils \
+             -L$(FFTWHOME)/lib -lfftw3 \
+             -L$(SLEPC_DIR)/$(PETSC_ARCH)/lib -lslepc \
+             -L$(PETSC_DIR)/$(PETSC_ARCH)/lib -lpetsc -lX11
+
+#######################################################################
+#            COILOPT++ Options
+#######################################################################
+  LCOILOPT = F
+  COILOPT_INC = -I$(COILOPT_PATH)
+  COILOPTPP_DIR = $(COILOPT_PATH)
+  LIB_COILOPTPP = libcoilopt++.a
+  COILOPT_LIB = $(COILOPT_PATH)/$(LIB_COILOPTPP) \
+                -L$(GSLHOME)/lib/x86_64-linux-gnu -lgsl -lgslcblas -lstdc++ -lmpi_cxx
+
+#######################################################################
+#            TERPSICHORE Options
+#######################################################################
+  LTERPSICHORE= F
+  TERPSICHORE_INC = -I$(TERPSICHORE_PATH)
+  TERPSICHORE_DIR = $(TERPSICHORE_PATH)
+  LIB_TERPSICHORE = libterpsichore.a
+  TERPSICHORE_LIB = $(TERPSICHORE_DIR)/$(LIB_TERPSICHORE)
+
+#######################################################################
+#            TRAVIS Options
+#######################################################################
+  LTRAVIS= F
+  TRAVIS_DIR = $(TRAVIS_PATH)
+  LIB_TRAVIS = libtravis64_sopt.a
+  LIB_MCONF  = libmconf64.a
+  TRAVIS_LIB = $(TRAVIS_DIR)/lib/$(LIB_TRAVIS) \
+               $(TRAVIS_DIR)/mag_conf/lib/$(LIB_MCONF) -lstdc++
+
+#######################################################################
+#            REGCOIL Options
+#######################################################################
+  LREGCOIL= F
+  REGCOIL_DIR = $(REGCOIL_PATH)
+  REGCOIL_INC = -I$(REGCOIL_DIR) 
+  LIB_REGCOIL = libregcoil.a
+  REGCOIL_LIB = $(REGCOIL_DIR)/$(LIB_REGCOIL) -fopenmp
+
+#######################################################################
+#            LIBSTELL Shared Options
+#######################################################################