Merge dev branch into master for release 0.2.0

Merge for release tag v0.2.0

TEST_CHECKPATCH_ALLOW_FAILURE=yes

Author: CamStan

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
-clocal.m4
+aclocal.m4
 autom4te.cache
 build
 config.*
@@ -48,16 +48,39 @@ log
 
 # project files
 server/src/unifycrd
+util/unifycr/src/unifycr
 
 # generated package files
 client/unifycr-config
 client/unifycr.pc
+extras/unifycr.conf
+libtool
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
+meta/src/Mlog2/.dirstamp
+t/sys/.dirstamp
 
 # test files
-client/tests/test_read_gotcha
-client/tests/test_read_static
-client/tests/test_write_gotcha
-client/tests/test_write_static
+client/unifycr-runtime-config.h
+examples/src/app-btio-gotcha
+examples/src/app-btio-static
+examples/src/app-mpiio-gotcha
+examples/src/app-mpiio-static
+examples/src/sysio-read-gotcha
+examples/src/sysio-read-static
+examples/src/app-tileio-gotcha
+examples/src/app-tileio-static
+examples/src/sysio-write-gotcha
+examples/src/sysio-write-static
+examples/src/sysio-writeread-gotcha
+examples/src/sysio-writeread-static
+examples/src/sysio-writeread2-gotcha
+examples/src/sysio-writeread2-static
+examples/src/app-hdf5-create-gotcha
+examples/src/app-hdf5-writeread-gotcha
 t/sys/open.t
 t/test-results/
 t/unifycr_unmount.t

.gitignore

@@ -6,15 +6,24 @@ before_install:
   # MPI projects.
   - test -n $CC && unset CC
   - sudo apt-get -qq update
-  - sudo apt-get install --yes -qq build-essential autoconf libtool
+  - sudo apt-get install --yes -qq build-essential autoconf libtool cmake
   - sudo apt-get install --yes -qq libopenmpi-dev openmpi-bin
+  - sudo apt-get install --yes -qq libhdf5-openmpi-dev
   - (cd $HOME/spack; git describe) || git clone https://github.com/spack/spack $HOME/spack
-  - $HOME/spack/bin/spack install leveldb
-  - $HOME/spack/bin/spack install gotcha
   - $HOME/spack/bin/spack install environment-modules
+  - $HOME/spack/bin/spack install leveldb
+  - $HOME/spack/bin/spack install [email protected]
+  - $HOME/spack/bin/spack install flatcc
+  # insall margo with spack
+  - git config --global http.sslVerify false
+  - git clone https://xgitlab.cels.anl.gov/sds/sds-repo.git $HOME/sds-repo.git
+  - $HOME/spack/bin/spack repo add $HOME/sds-repo.git
+  - $HOME/spack/bin/spack install margo
+  - git config --global http.sslVerify true
+  # prepare build environment
   - . $HOME/spack/share/spack/setup-env.sh
   - spack load environment-modules
-  - source <(spack module loads gotcha leveldb)
+  - source <(spack module tcl loads leveldb gotcha@0.0.2 flatcc mercury argobots margo)
   - eval $(./scripts/git_log_test_env.sh)
   - export TEST_CHECKPATCH_SKIP_FILES
 
@@ -29,7 +38,9 @@ before_cache:
 script:
   # Force git to update the shallow clone and include tags so git-describe works
   - git fetch --unshallow --tags
-  - sh autogen.sh && ./configure && make -k && make distcheck
+  - sh autogen.sh
+  - ./configure || cat config.log
+  - make -k && make distcheck
   - ./scripts/checkpatch.sh || test "$TEST_CHECKPATCH_ALLOW_FAILURE" = yes
 
 after_failure:

.travis.yml

@@ -1,4 +1,4 @@
-SUBDIRS = meta server client t
+SUBDIRS = common meta server client examples extras t util
 
 CONFIG = ordered
 

Makefile.am

@@ -17,16 +17,17 @@ scalable metadata indexing, co-located I/O delegation, and server-side read
 clustering and pipelining.
 
 ## Documentation
-Full UnifyCR documentation is contained [here](http://unifycr.readthedocs.io).
+Full UnifyCR documentation is contained [here](https://unifycr.readthedocs.io).
 
-Use [Build & I/O Interception](http://unifycr.readthedocs.io/en/latest/build-intercept.html)
+Use [Build & I/O Interception](http://unifycr.readthedocs.io/en/dev/build-intercept.html)
 for instructions on how to build and install UnifyCR.
 
 ## Build Status
 The current status of the UnifyCR dev branch is:
 
 [![Build Status](https://api.travis-ci.org/LLNL/UnifyCR.png?branch=dev)](https://travis-ci.org/LLNL/UnifyCR)
+[![Read the Docs](https://readthedocs.org/projects/unifycr/badge/?version=dev)](https://unifycr.readthedocs.io)
 
 ## Contribute and Develop
-We have a separate document with
-[contribution guidelines](./.github/CONTRIBUTING.md).
+Contributing guidelines can be found in our
+[documentation](https://unifycr.readthedocs.io/en/dev/style-guides.html).

README.md

@@ -1,4 +1,4 @@
-SUBDIRS = src tests
+SUBDIRS = src
 
 bin_SCRIPTS = unifycr-config
 

client/Makefile.am

@@ -12,50 +12,6 @@ They are also used to generate the code required for GOTCHA.
 - unifycr_list.txt - list of wrappers in UnifyCR
 - unifycr_unsupported_list.txt - list of wrappers in UnifyCR that implemented, but not supported
 
-# Running the unifycr_check_fns tool
-
-This tool identifies the set of I/O calls used in an application by running nm on the executable.
-It reports any I/O routines used by the app, which are not supported by UnifyCR.
-If an application uses an I/O routine that is not supported, it likely cannot use UnifyCR.
-If the tool does not report unsupported wrappers,
-the app may work with UnifyCR but it is not guaranteed to work.
-
-    unifycr_check_fns <executable>
-
-# Building the GOTCHA list
-
-The gotcha_map_unifycr_list.h file contains the code necessary to wrap I/O functions with GOTCHA.
-This is generated from the unifycr_list.txt file by running the following command:
-
-    python unifycr_translate.py unifycr_list
-
-# Commands to build files
-
-## fakechroot_list.txt
-The fakechroot_list.txt file lists I/O routines implemented in fakechroot.
-This list was generated using the following commands:
-
-    git clone https://github.com/fakechroot/fakechroot.git fakechroot.git
-    cd fakechroot.git/src
-    ls *.c > fakechroot_list.txt
-
-## gnulibc_list.txt
-The gnulibc_list.txt file lists I/O routines available in libc.
-This list was writte by hand using information from
-[http://www.gnu.org/software/libc/manual/html_node/I_002fO-Overview.html#I_002fO-Overview](http://www.gnu.org/software/libc/manual/html_node/I_002fO-Overview.html#I_002fO-Overview).
-
-## cstdio_list.txt
-The cstdio_list.txt file lists I/O routines available in libstdio..
-This list was written by hand using information from
-[http://www.open-std.org/jtc1/sc22/wg14/www/docs/n1124.pdf](http://www.open-std.org/jtc1/sc22/wg14/www/docs/n1124.pdf).
-
-## unifycr_list.txt
-The unifycr_list.txt file specifies the set of wrappers in UnifyCR.
-Most but not all such wrappers are supported.
-The command to build unifycr list:
-
-    grep UNIFYCR_WRAP ../src/*.c > unifycr_list.txt
-
-## unifycr_unsupported_list.txt
-The unify_unsupported_list.txt file specifies wrappers that are in UnifyCR, but are known to not actually be supported.
-This list is written by hand.
+Our [Wrapper Guide](https://unifycr.readthedocs.io/en/dev/wrappers.html)
+has the full documentation on running the unifycr_check_fns tool, building the
+GOTCHA list, and building the other .txt files here.