diff --git a/README.md b/README.md
index 19e862520bd00ea9303c221780805780ad94e638..7f2e8d1d830c54fcc41b0315f8560b15d4f27626 100644
--- a/README.md
+++ b/README.md
@@ -59,17 +59,12 @@ Check help for more options:
```
$ ogscm --help
-usage: ogscm [-h] [--version] [--out OUT] [--file FILE] [--print]
- [--format [{docker,singularity} [{docker,singularity} ...]]]
- [--pm [{system,conan,spack,off} [{system,conan,spack,off} ...]]]
- [--ompi [OMPI [OMPI ...]]] [--ogs [OGS [OGS ...]]]
- [--cmake_args [CMAKE_ARGS [CMAKE_ARGS ...]]] [--build]
- [--upload] [--registry REGISTRY] [--convert] [--runtime-only]
- [--ccache] [--parallel PARALLEL] [--base_image BASE_IMAGE]
- [--compiler COMPILER] [--compiler_version COMPILER_VERSION]
- [--gui] [--docs] [--jenkins] [--cvode] [--cppcheck] [--iwyy]
- [--gcovr] [--mpi_benchmarks] [--dev] [--insitu]
- [--pip [package [package ...]]] [--clean] [--deploy [DEPLOY]]
+usage: ogscm [-h] [--version] [--out OUT] [--file FILE] [--print] [--format [{docker,singularity} [{docker,singularity} ...]]]
+ [--pm [{system,conan,spack,off} [{system,conan,spack,off} ...]]] [--ompi [OMPI [OMPI ...]]] [--ogs [OGS [OGS ...]]]
+ [--cmake_args [CMAKE_ARGS [CMAKE_ARGS ...]]] [--build] [--upload] [--registry REGISTRY] [--tag TAG] [--convert] [--runtime-only] [--ccache]
+ [--parallel PARALLEL] [--base_image BASE_IMAGE] [--compiler COMPILER] [--compiler_version COMPILER_VERSION] [--gui] [--docs] [--jenkins]
+ [--gitlab] [--cvode] [--cppcheck] [--iwyy] [--gcovr] [--mpi_benchmarks] [--dev] [--insitu] [--pip [package [package ...]]]
+ [--packages [packages [packages ...]]] [--clean] [--deploy [DEPLOY]]
optional arguments:
-h, --help show this help message and exit
@@ -83,69 +78,56 @@ Combinatorial options:
--format [{docker,singularity} [{docker,singularity} ...]]
--pm [{system,conan,spack,off} [{system,conan,spack,off} ...]]
- Package manager to install third-party dependencies
- (default: ['conan'])
+ Package manager to install third-party dependencies (default: ['conan'])
--ompi [OMPI [OMPI ...]]
- OpenMPI version, e.g. 2.1.1, 2.1.5, 3.0.1, 3.1.2
- (default: ['off'])
+ OpenMPI version, e.g. 2.1.1, 2.1.5, 3.0.1, 3.1.2 (default: ['off'])
--ogs [OGS [OGS ...]]
- OGS GitHub repo in the form 'user/repo@branch' OR
- 'user/repo@@commit' to checkout a specific commit OR a
- path to a local subdirectory to the git cloned OGS
- sourcesOR 'off' to disable OGS building (default:
- ['ufz/ogs@master'])
+ OGS GitHub repo in the form 'user/repo@branch' OR 'user/repo@@commit' to checkout a specific commit OR a path to a local subdirectory
+ to the git cloned OGS sources OR 'off' to disable OGS building (default: ['ufz/ogs@master'])
--cmake_args [CMAKE_ARGS [CMAKE_ARGS ...]]
- CMake argument sets have to be quoted and **must**
- start with a space. e.g. --cmake_args ' -DFIRST=TRUE
- -DFOO=BAR' ' -DSECOND=TRUE' (default: [''])
+ CMake argument sets have to be quoted and **must** start with a space. e.g. --cmake_args ' -DFIRST=TRUE -DFOO=BAR' ' -DSECOND=TRUE'
+ (default: [''])
Image build options:
- --build, -B Build the images from the definition files (default:
- False)
+ --build, -B Build the images from the definition files (default: False)
--upload, -U Upload Docker image to registry (default: False)
- --registry REGISTRY The docker registry the image is tagged and uploaded
- to. (default: registry.opengeosys.org/ogs/ogs)
- --convert, -C Convert Docker image to Singularity image (default:
- False)
- --runtime-only, -R Generate multi-stage Dockerfiles for small runtime
- images (default: False)
+ --registry REGISTRY The docker registry the image is tagged and uploaded to. (default: registry.opengeosys.org/ogs/ogs)
+ --tag TAG The full docker image tag. Overwrites --registry. (default: )
+ --convert, -C Convert Docker image to Singularity image (default: False)
+ --runtime-only, -R Generate multi-stage Dockerfiles for small runtime images (default: False)
--ccache Enables ccache build caching. (default: False)
--parallel PARALLEL, -j PARALLEL
- The number of cores to use for compilation. (default:
- 10)
+ The number of cores to use for compilation. (default: 10)
Additional options:
--base_image BASE_IMAGE
- The base image. (default: ubuntu:18.04)
- --compiler COMPILER The compiler to use. Possible options: off, gcc, clang
- (default: gcc)
+ The base image. (centos:8 is supported too) (default: ubuntu:19.10)
+ --compiler COMPILER The compiler to use. Possible options: off, gcc, clang (default: gcc)
--compiler_version COMPILER_VERSION
Compiler version. (default: )
--gui Builds the GUI (Data Explorer) (default: False)
- --docs Setup documentation requirements (Doxygen) (default:
- False)
+ --docs Setup documentation requirements (Doxygen) (default: False)
--jenkins Setup Jenkins slave (default: False)
+ --gitlab Setup for GitLab-CI (default: False)
--cvode Install and configure with cvode (default: False)
--cppcheck Install cppcheck (default: False)
--iwyy Install include-what-you-use (default: False)
--gcovr Install gcovr (default: False)
- --mpi_benchmarks Installs OSU MPI benchmarks as scif app and mpi_bw,
- mpi_ring,mpi_hello (default: False)
+ --mpi_benchmarks Installs OSU MPI benchmarks as scif app and mpi_bw, mpi_ring,mpi_hello (default: False)
--dev Installs development tools (vim, gdb) (default: False)
--insitu Builds with insitu capabilities (default: False)
--pip [package [package ...]]
- Install additional Python packages (default: [''])
+ Install additional Python packages (default: [])
+ --packages [packages [packages ...]]
+ Install additional OS packages (default: [])
Maintenance:
- --clean Cleans up generated files in default directories.
- (default: False)
+ --clean Cleans up generated files in default directories. (default: False)
Image deployment:
--deploy [DEPLOY], -D [DEPLOY]
- Deploys to all configured hosts (in
- config/deploy_hosts.yml) with no additional arguments
- or to the specified host. Implies --build and
- --convert arguments. (default: )
+ Deploys to all configured hosts (in config/deploy_hosts.yml) with no additional arguments or to the specified host. Implies --build
+ and --convert arguments. (default: )
```
## Advanced usage
diff --git a/ogscm/building_blocks/ogs.py b/ogscm/building_blocks/ogs.py
index bf6c893daf5b61d16d9846bbe2385d47a69e06e7..94f6352f19624fb5f5c3903999e8d8fa7d7d8085 100644
--- a/ogscm/building_blocks/ogs.py
+++ b/ogscm/building_blocks/ogs.py
@@ -112,7 +112,7 @@ class ogs(bb_base, hpccm.templates.CMakeBuild, hpccm.templates.rm):
self.__cmake_args.append("-DOGS_USE_PETSC=ON")
if conan:
self.__cmake_args.append("-DOGS_CONAN_USE_SYSTEM_OPENMPI=ON")
- if conan:
+ if not conan:
self.__cmake_args.append('-DOGS_USE_CONAN=OFF')
# Configure and build
diff --git a/ogscm/building_blocks/ogs_base.py b/ogscm/building_blocks/ogs_base.py
index 7c3d1bf6e9e03943f9a320295bda4ac6bfc302e8..d9896cc12baf004300ff09ed107df25b19c8a1ae 100644
--- a/ogscm/building_blocks/ogs_base.py
+++ b/ogscm/building_blocks/ogs_base.py
@@ -40,7 +40,7 @@ class ogs_base(bb_base):
packages=['virtualenv', 'pre-commit', 'cmake-format'])
self += packages(ospackages=self.__ospackages,
apt_ppas=['ppa:git-core/ppa'],
- epel=True)
+ epel=True, powertools=True)
self += shell(commands=self.__commands)
def __setup(self):
diff --git a/ogscm/cli.py b/ogscm/cli.py
index 1ee7e91749093aa62676b821db39e836a62941f5..5310bec589eecc24f8d2ce35c0faa70f33ff5200 100644
--- a/ogscm/cli.py
+++ b/ogscm/cli.py
@@ -284,7 +284,7 @@ def main(): # pragma: no cover
# LD_LIBRARY_PATH) as host var overwrites container var. See
# https://github.com/sylabs/singularity/pull/2669
# Stage0 += boost(version='1.66.0') # header only?
- Stage0 += packages(ospackages=['libboost-dev'])
+ Stage0 += packages(apt=['libboost-dev'], yum=['boost-devel'], epel=True)
# Stage0 += environment(variables={'BOOST_ROOT': '/usr/local/boost'})
Stage0 += eigen()
vtk_cmake_args = [
@@ -293,13 +293,20 @@ def main(): # pragma: no cover
'-DVTK_Group_StandAlone=OFF'
]
if args.gui:
- Stage0 += packages(ospackages=[
- 'libgeotiff-dev',
- 'libqt5x11extras5-dev',
- 'libqt5xmlpatterns5-dev',
- 'libshp-dev',
- 'qt5-default'
- ])
+ Stage0 += packages(apt=[
+ 'libgeotiff-dev',
+ 'libshp-dev',
+ 'libqt5x11extras5-dev',
+ 'libqt5xmlpatterns5-dev',
+ 'qt5-default'
+ ],
+ yum=[
+ 'libgeotiff-devel',
+ 'shapelib-devel',
+ 'qt5-qtbase',
+ 'qt5-qtxmlpatterns',
+ 'qt5-qtx11extras'
+ ])
vtk_cmake_args = [
'-DVTK_BUILD_QT_DESIGNER_PLUGIN=OFF',
'-DVTK_Group_Qt=ON',
@@ -358,11 +365,14 @@ def main(): # pragma: no cover
Stage0 += raw(docker=f"ARG OGS_COMMIT_HASH={info.commit_hash}")
scif_file = f"{info.out_dir}/ogs.scif"
+ definition_file_path = os.path.join(info.out_dir, info.definition_file)
if info.ogsdir:
context_path_size = len(ogs_version)
+ print(f"chdir to {ogs_version}")
os.chdir(ogs_version)
mount_args = f'{mount_args} --mount=type=bind,target=/scif/apps/ogs/src,rw'
scif_file = f"{info.out_dir[context_path_size+1:]}/ogs.scif"
+ definition_file_path = f"{info.out_dir[context_path_size+1:]}/{info.definition_file}"
ogs_app = scif(_arguments=mount_args, name='ogs', file=scif_file)
ogs_app += ogs(repo=info.repo,
@@ -391,14 +401,12 @@ def main(): # pragma: no cover
stages_string += "\n\n" + str(Stage1)
# ---------------------------- recipe end -----------------------------
-
- definition_file_path = os.path.join(info.out_dir, info.definition_file)
with open(definition_file_path, 'w') as f:
print(stages_string, file=f)
if args.print:
print(stages_string)
else:
- print(f'Created definition {definition_file_path}')
+ print(f'Created definition {os.path.abspath(definition_file_path)}')
# Create image
if not args.build:
@@ -417,8 +425,6 @@ def main(): # pragma: no cover
build_cmd = (f"DOCKER_BUILDKIT=1 docker build "
f"-t {info.tag} -f {definition_file_path} .")
- if info.ogsdir:
- build_cmd = "(cd {0} && {1})".format(ogs_version, build_cmd)
print(f"Running: {build_cmd}")
subprocess.run(build_cmd, shell=True)
inspect_out = subprocess.check_output(
diff --git a/ogscm/cli_args.py b/ogscm/cli_args.py
index d08a771acfb9f535ebabe9c59f4b3f7b3768c443..5d6e528a2a4532a6cd82646f1e92fedf882124af 100644
--- a/ogscm/cli_args.py
+++ b/ogscm/cli_args.py
@@ -126,7 +126,7 @@ class Cli_Args(argparse.ArgumentParser):
switches_g.add_argument('--base_image',
type=str,
default='ubuntu:19.10',
- help='The base image.')
+ help='The base image. (centos:8 is supported too)')
switches_g.add_argument(
'--compiler',
type=str,