Closed whedon closed 2 years ago
Overall, I have preferred the Dockerized solution to getting started with NLMech, since this avoids the need for a user to build and install all these complex TPLs. You can add the build all TPLs from source as part of the developer guide or for advanced users since it would take a non-trivial amount of time to get it built, on some user machine.
Yes, I totally agree that we have some complex TPLs, and it is not easy to install the code. As you said, we provide the docker image for people who just want to play with the code.
@Kevin-Mattheus-Moerman My review of NLMech is complete. Apart from some hiccups in the installation process from source, I do not have any other pending issues as @diehlpk has promptly addressed all the concerns I raised here, and at NLMech issue #131. I recommend acceptance of the submission once all the other reviews are in. Sorry about the longer than average delay in getting my review done.
Use of module commands in the build scripts prevent installations on personal computers which usually do not have module management software installed on them.
@chennachaos That is not correct, since the scripts generates the modules for you, but there is not need to use them to run the code.
Hi @diehlpk, I don't understand how the installation can be carried out if module command is not available.
I would like to finish the review by the end of this week. Do you have any other method that I can follow to install and test the code on my PC? I have Ubuntu 20.04.
Hi @diehlpk, I don't understand how the installation can be carried out if module command is not available.
I would like to finish the review by the end of this week. Do you have any other method that I can follow to install and test the code on my PC? I have Ubuntu 20.04.
Hey @chennachaos you can just run the scripts, as I showed above. They do not use the module command at all. The scripts just write modules file, you can use on clusters, but they are optional. I had to use modules on on cluster to find linked libraries.
I think if you follow these instructions on your Ubuntu, you can compile the code:
And I had to install the following packages using apt-get
After that I run
git clone https://github.com/nonlocalmodels/HPCBuildInfrastructure.git cd HPCBuildInfrastructure
and executed the following commands to build all dependencies:
I think this is what you need to do to compile the code. If you install vtk or boost using ap-get, you can skip the build-all.sh for them and CMake will use the one installed on the system.
I can test it on Ubuntu with the installed vtk and boost library, but it worked on Fedora out of the box.
Hi @diehlpk. I managed to install all the dependencies using the commands you provided. Thanks!
I encountered some errors while building the NLMech library. The error is due to CMake being unable to find the path to the HPX library/package. How can I fix this?
Hi @diehlpk. I managed to install all the dependencies using the commands you provided. Thanks!
I encountered some errors while building the NLMech library. The error is due to CMake being unable to find the path to the HPX library/package. How can I fix this? @chennachaos I added a new script
./build-all.sh Release without-gcc nl
and you should please use this script to compile the code. This script will set the path to all installed libraries using the previous scripts.
I pulled the new file. I am getting the same error even with ./build-all.sh Release without-gcc nl. The problem is in the installation of dependencies. In particular, the directories and other environment variables do not seem to be set properly.
I pulled the new file. I am getting the same error even with ./build-all.sh Release without-gcc nl. The problem is in the installation of dependencies. In particular, the directories and other environment variables do not seem to be set properly.
@chennachaos Can you please post the error to help me to check what is going wrong?
@diehlpk, this is the screen output.
-- The CXX compiler identification is GNU 9.3.0 -- The C compiler identification is GNU 9.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done CMake Error at CMakeLists.txt:67 (find_package): By not providing "FindHPX.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "HPX", but CMake did not find one.
Could not find a package configuration file provided by "HPX" with any of the following names:
HPXConfig.cmake
hpx-config.cmake
Add the installation prefix of "HPX" to CMAKE_PREFIX_PATH or set "HPX_DIR" to a directory containing one of the above files. If "HPX" provides a separate development package or SDK, be sure it has been installed.
-- Configuring incomplete, errors occurred! See also "/home/chenna/Documents/HPCBuildInfrastructure/src/nl/NLMech/build/CMakeFiles/CMakeOutput.log".
@chennachaos Can you please do a `ls -lah build' in the ain folder, I would like to see if all libs were compiled?
@chennachaos Can you list the content of the folder /hpx/lib64/cmake/HPX
thanks?
@diehlpk, see below for the out of ls commands.
chenna@chenna-XPS-L501X:~/Documents/HPCBuildInfrastructure$ ls -lah build
total 48K
drwxrwxr-x 12 chenna chenna 4.0K Jul 27 13:43 .
drwxrwxr-x 6 chenna chenna 4.0K Jul 29 17:26 ..
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:03 blaze
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:04 blaze-iterative
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:08 boost
drwxrwxr-x 6 chenna chenna 4.0K Jul 27 10:54 cmake
drwxrwxr-x 7 chenna chenna 4.0K Jul 27 11:51 hpx
drwxrwxr-x 9 chenna chenna 4.0K Jul 27 11:00 hwloc
drwxr-xr-x 6 chenna chenna 4.0K Jul 27 11:02 jemalloc
drwxrwxr-x 10 chenna chenna 4.0K Jul 27 13:43 modules
drwxrwxr-x 6 chenna chenna 4.0K Jul 27 13:43 vtk
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:14 yamlcpp
chenna@chenna-XPS-L501X:~/Documents/HPCBuildInfrastructure$ ls -lah build/hpx/lib/cmake/HPX/
total 664K
drwxr-xr-x 5 chenna chenna 4.0K Jul 27 11:51 .
drwxrwxr-x 3 chenna chenna 4.0K Jul 27 11:51 ..
-rw-r--r-- 1 chenna chenna 2.1K Jul 27 11:20 FindAmplifier.cmake
-rw-r--r-- 1 chenna chenna 564 Jul 27 11:20 FindBreathe.cmake
-rw-r--r-- 1 chenna chenna 2.4K Jul 27 11:20 FindBZip2.cmake
-rw-r--r-- 1 chenna chenna 3.0K Jul 27 11:20 FindGooglePerftools.cmake
-rw-r--r-- 1 chenna chenna 2.2K Jul 27 11:20 FindHwloc.cmake
-rw-r--r-- 1 chenna chenna 1.8K Jul 27 11:20 FindIbverbs.cmake
-rw-r--r-- 1 chenna chenna 1.1K Jul 27 11:20 FindIB_VERBS.cmake
-rw-r--r-- 1 chenna chenna 2.7K Jul 27 11:20 FindJemalloc.cmake
-rw-r--r-- 1 chenna chenna 1.4K Jul 27 11:20 FindLibfabric.cmake
-rw-r--r-- 1 chenna chenna 1.9K Jul 27 11:20 FindLibSigSegv.cmake
-rw-r--r-- 1 chenna chenna 1.6K Jul 27 11:20 FindMSR.cmake
-rw-r--r-- 1 chenna chenna 1.7K Jul 27 11:20 FindOrangeFS.cmake
-rw-r--r-- 1 chenna chenna 2.2K Jul 27 11:20 FindPAPI.cmake
-rw-r--r-- 1 chenna chenna 1.7K Jul 27 11:20 FindPMI.cmake
-rw-r--r-- 1 chenna chenna 1.7K Jul 27 11:20 FindQThreads.cmake
-rw-r--r-- 1 chenna chenna 1.4K Jul 27 11:20 FindRdmacm.cmake
-rw-r--r-- 1 chenna chenna 1.1K Jul 27 11:20 FindRDMA_CM.cmake
-rw-r--r-- 1 chenna chenna 1.4K Jul 27 11:20 FindSnappy.cmake
-rw-r--r-- 1 chenna chenna 525 Jul 27 11:20 FindSphinx.cmake
-rw-r--r-- 1 chenna chenna 1.5K Jul 27 11:20 FindTBB.cmake
-rw-r--r-- 1 chenna chenna 2.4K Jul 27 11:20 FindTBBmalloc.cmake
-rw-r--r-- 1 chenna chenna 1.9K Jul 27 11:20 FindTCMalloc.cmake
-rw-r--r-- 1 chenna chenna 1.1K Jul 27 11:20 FindValgrind.cmake
-rw-r--r-- 1 chenna chenna 9.5K Jul 27 11:20 GitExternal.cmake
-rw-r--r-- 1 chenna chenna 7.0K Jul 27 11:20 HPX_AddCompileFlag.cmake
-rw-r--r-- 1 chenna chenna 5.5K Jul 27 11:20 HPX_AddCompileTest.cmake
-rw-r--r-- 1 chenna chenna 9.7K Jul 27 11:20 HPX_AddComponent.cmake
-rw-r--r-- 1 chenna chenna 19K Jul 27 11:20 HPX_AddConfigTest.cmake
-rw-r--r-- 1 chenna chenna 6.3K Jul 27 11:20 HPX_AddDefinitions.cmake
-rw-r--r-- 1 chenna chenna 7.0K Jul 27 11:20 HPX_AddExecutable.cmake
-rw-r--r-- 1 chenna chenna 8.8K Jul 27 11:20 HPX_AddLibrary.cmake
-rw-r--r-- 1 chenna chenna 2.6K Jul 27 11:20 HPX_AddLibraryHeaders.cmake
-rw-r--r-- 1 chenna chenna 2.4K Jul 27 11:20 HPX_AddLibrarySources.cmake
-rw-r--r-- 1 chenna chenna 3.0K Jul 27 11:20 HPX_AddLinkFlag.cmake
-rw-r--r-- 1 chenna chenna 11K Jul 27 11:20 HPX_AddModule.cmake
-rw-r--r-- 1 chenna chenna 2.1K Jul 27 11:20 HPX_AddParcelport.cmake
-rw-r--r-- 1 chenna chenna 1.2K Jul 27 11:20 HPX_AddPseudoDependencies.cmake
-rw-r--r-- 1 chenna chenna 754 Jul 27 11:20 HPX_AddPseudoTarget.cmake
-rw-r--r-- 1 chenna chenna 1.7K Jul 27 11:20 HPX_AddSourceGroup.cmake
-rw-r--r-- 1 chenna chenna 7.6K Jul 27 11:20 HPX_AddTest.cmake
-rw-r--r-- 1 chenna chenna 521 Jul 27 11:20 HPX_AppendProperty.cmake
-rw-r--r-- 1 chenna chenna 24K Jul 27 11:21 HPXCacheVariables.cmake
-rw-r--r-- 1 chenna chenna 2.3K Jul 27 11:20 HPX_CheckCXXStandard.cmake
-rw-r--r-- 1 chenna chenna 1.5K Jul 27 11:20 HPX_CompilerFlagsTargets.cmake
-rw-r--r-- 1 chenna chenna 3.9K Jul 27 11:21 HPXConfig.cmake
-rw-r--r-- 1 chenna chenna 1.4K Jul 27 11:21 HPXConfigVersion.cmake
-rw-r--r-- 1 chenna chenna 1.3K Jul 27 11:20 HPX_CreateSymbolicLink.cmake
-rw-r--r-- 1 chenna chenna 322 Jul 27 11:20 HPX_CXXOverrides.cmake
-rw-r--r-- 1 chenna chenna 1.7K Jul 27 11:20 HPX_Documentation.cmake
-rw-r--r-- 1 chenna chenna 874 Jul 27 11:20 HPX_ExportTargets.cmake
-rw-r--r-- 1 chenna chenna 587 Jul 27 11:20 HPX_ForceOutOfTreeBuild.cmake
-rw-r--r-- 1 chenna chenna 417 Jul 27 11:20 HPX_FortranCompiler.cmake
-rw-r--r-- 1 chenna chenna 368 Jul 27 11:20 HPX_FortranOverrides.cmake
-rw-r--r-- 1 chenna chenna 1.3K Jul 27 11:20 HPX_ForwardCacheVariables.cmake
-rw-r--r-- 1 chenna chenna 5.3K Jul 27 11:20 HPX_GeneratePackage.cmake
-rw-r--r-- 1 chenna chenna 13K Jul 27 11:20 HPX_GeneratePackageUtils.cmake
-rw-r--r-- 1 chenna chenna 1.3K Jul 27 11:20 HPX_GitCommit.cmake
-rw-r--r-- 1 chenna chenna 765 Jul 27 11:20 HPX_HandleComponentDependencies.cmake
-rw-r--r-- 1 chenna chenna 328 Jul 27 11:20 HPX_Include.cmake
-rw-r--r-- 1 chenna chenna 61K Jul 27 11:21 HPXInternalTargets.cmake
-rw-r--r-- 1 chenna chenna 43K Jul 27 11:21 HPXInternalTargets-release.cmake
-rw-r--r-- 1 chenna chenna 5.2K Jul 27 11:21 HPXMacros.cmake
-rw-r--r-- 1 chenna chenna 2.7K Jul 27 11:20 HPX_Message.cmake
-rw-r--r-- 1 chenna chenna 3.4K Jul 27 11:20 HPX_Option.cmake
-rw-r--r-- 1 chenna chenna 3.6K Jul 27 11:20 HPX_PerformCxxFeatureTests.cmake
-rw-r--r-- 1 chenna chenna 3.2K Jul 27 11:20 HPX_PrintSummary.cmake
-rw-r--r-- 1 chenna chenna 357 Jul 27 11:20 HPX_SetCMakePolicy.cmake
-rw-r--r-- 1 chenna chenna 463 Jul 27 11:20 HPX_SetFullRPATH.cmake
-rw-r--r-- 1 chenna chenna 980 Jul 27 11:20 HPX_SetLibName.cmake
-rw-r--r-- 1 chenna chenna 1.6K Jul 27 11:20 HPX_SetOutputPaths.cmake
-rw-r--r-- 1 chenna chenna 1.2K Jul 27 11:20 HPX_SetPlatform.cmake
-rw-r--r-- 1 chenna chenna 5.4K Jul 27 11:20 HPX_SetupAllocator.cmake
-rw-r--r-- 1 chenna chenna 2.7K Jul 27 11:20 HPX_SetupApex.cmake
-rw-r--r-- 1 chenna chenna 4.5K Jul 27 11:20 HPX_SetupBoost.cmake
-rw-r--r-- 1 chenna chenna 1.1K Jul 27 11:20 HPX_SetupBoostFilesystem.cmake
-rw-r--r-- 1 chenna chenna 642 Jul 27 11:20 HPX_SetupBoostIostreams.cmake
-rw-r--r-- 1 chenna chenna 835 Jul 27 11:20 HPX_SetupBoostProgramOptions.cmake
-rw-r--r-- 1 chenna chenna 608 Jul 27 11:20 HPX_SetupBoostRegex.cmake
-rw-r--r-- 1 chenna chenna 2.4K Jul 27 11:20 HPX_SetupCUDA.cmake
-rw-r--r-- 1 chenna chenna 935 Jul 27 11:20 HPX_SetupGooglePerfTools.cmake
-rw-r--r-- 1 chenna chenna 1.5K Jul 27 11:20 HPX_SetupHpxmp.cmake
-rw-r--r-- 1 chenna chenna 745 Jul 27 11:20 HPX_SetupHwloc.cmake
-rw-r--r-- 1 chenna chenna 1.5K Jul 27 11:20 HPX_SetupLibCDS.cmake
-rw-r--r-- 1 chenna chenna 11K Jul 27 11:20 HPX_SetupLibfabric.cmake
-rw-r--r-- 1 chenna chenna 1.9K Jul 27 11:20 HPX_SetupMPI.cmake
-rw-r--r-- 1 chenna chenna 813 Jul 27 11:20 HPX_SetupPapi.cmake
-rw-r--r-- 1 chenna chenna 5.8K Jul 27 11:20 HPX_SetupTarget.cmake
-rw-r--r-- 1 chenna chenna 1.1K Jul 27 11:20 HPX_SetupValgrind.cmake
-rw-r--r-- 1 chenna chenna 3.1K Jul 27 11:20 HPX_SetupVc.cmake
-rw-r--r-- 1 chenna chenna 9.2K Jul 27 11:20 HPX_SetupVerbs.cmake
-rw-r--r-- 1 chenna chenna 976 Jul 27 11:20 HPX_ShortenPseudoTarget.cmake
-rw-r--r-- 1 chenna chenna 7.1K Jul 27 11:21 HPXTargets.cmake
-rw-r--r-- 1 chenna chenna 4.7K Jul 27 11:21 HPXTargets-release.cmake
-rw-r--r-- 1 chenna chenna 5.7K Jul 27 11:20 HPX_UpdateGitDocs.cmake
-rw-r--r-- 1 chenna chenna 632 Jul 27 11:20 HPX_Utils.cmake
-rw-r--r-- 1 chenna chenna 4.8K Jul 27 11:20 installed_hpx.cmake
drwxr-xr-x 2 chenna chenna 4.0K Jul 27 11:51 scripts
-rw-r--r-- 1 chenna chenna 5.9K Jul 27 11:20 TargetArch.cmake
drwxr-xr-x 2 chenna chenna 4.0K Jul 27 11:51 tests
drwxr-xr-x 2 chenna chenna 4.0K Jul 27 11:51 toolchains
@chennachaos Thanks for posting the output and I found the issues with the path
Can you please for now remove the 64 in lib64, and you should be able to compile the code. I will debug later this week why this issue with the 64 happens.
Hi @diehlpk. I changed the line you suggested. I also had to make a similar change at line 34 for the vtk library. After this, I got the following error. The issue is in locating the GMSH library.
CMake Error at cmake/FindGmsh.cmake:19 (message):
Gmsh Library not found: Specify the GMSH_DIR where Gmsh is located
Call Stack (most recent call first):
CMakeLists.txt:87 (find_package)
-- Configuring incomplete, errors occurred!
See also "/home/chenna/Documents/HPCBuildInfrastructure/src/nl/NLMech/build/CMakeFiles/CMakeOutput.log".
See also "/home/chenna/Documents/HPCBuildInfrastructure/src/nl/NLMech/build/CMakeFiles/CMakeError.log".
Hi @diehlpk. I changed the line you suggested. I also had to make a similar change at line 34 for the vtk library. After this, I got the following error. The issue is in locating the GMSH library.
CMake Error at cmake/FindGmsh.cmake:19 (message): Gmsh Library not found: Specify the GMSH_DIR where Gmsh is located Call Stack (most recent call first): CMakeLists.txt:87 (find_package) -- Configuring incomplete, errors occurred! See also "/home/chenna/Documents/HPCBuildInfrastructure/src/nl/NLMech/build/CMakeFiles/CMakeOutput.log". See also "/home/chenna/Documents/HPCBuildInfrastructure/src/nl/NLMech/build/CMakeFiles/CMakeError.log".
@chennachaos I checked the ls of the build folder you provided
chenna@chenna-XPS-L501X:~/Documents/HPCBuildInfrastructure$ ls -lah build
total 48K
drwxrwxr-x 12 chenna chenna 4.0K Jul 27 13:43 .
drwxrwxr-x 6 chenna chenna 4.0K Jul 29 17:26 ..
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:03 blaze
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:04 blaze-iterative
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:08 boost
drwxrwxr-x 6 chenna chenna 4.0K Jul 27 10:54 cmake
drwxrwxr-x 7 chenna chenna 4.0K Jul 27 11:51 hpx
drwxrwxr-x 9 chenna chenna 4.0K Jul 27 11:00 hwloc
drwxr-xr-x 6 chenna chenna 4.0K Jul 27 11:02 jemalloc
drwxrwxr-x 10 chenna chenna 4.0K Jul 27 13:43 modules
drwxrwxr-x 6 chenna chenna 4.0K Jul 27 13:43 vtk
drwxrwxr-x 4 chenna chenna 4.0K Jul 27 11:14 yamlcpp
I can not find a gmsh
folder there, so could it be that you did not compile gmsh using
./build-all.sh Release without-gcc gmsh
or installed the gmsh-devel
package?
@diehlpk, that's correct! GMSH is not part of your build system. That is why I didn't install GMSH with ./build-all.sh Release without-gcc gmsh. There is no build-gmsh.sh file in the repo.
@chennachaos Ok, I added the script or you can use the system package.
@chennachaos can you provide an update on how this review is going? Has @diehlpk managed to address the issues you raised? Thanks!
Hi @Kevin-Mattheus-Moerman. I faced a lot of hurdles in installing the library. Some of the dependencies were missing and some scripts failed to work due to the issues with the pre-defined paths. @diehlpk has been prompt in answering my queries but I get the feeling that the installation procedure for such a small library is taking too long to test. This, I believe, is due to the use of new libraries which are not readily available as packages. I wanted to test the examples using the docker file but I don't have the docker installed on my computers at the moment. Even if docker works, the issues with the installation process should be addressed before the library can be recommended for publication so that it does not pose many hurdles for novice users.
Aside from the installation, I am happy with the rest of the library. I think, at this point, it would be good if you can have a look at the installation procedure and advise.
@chennachaos On Fedora, we have all packages, expect blaze_iterative
as system packages. You could run
dnf install -y \
hpx-devel \
cmake \
blaze-devel \
vtk-devel \
yaml-cpp-devel \
doxygen \
graphviz \
git \
libXext-devel \
gmsh-devel \
metis-devel \
gcovr \
python3 \
python3-pip \
gmsh-devel \
rpm-build \
pcl-devel
dnf install @development-tools -y
git clone https://github.com/STEllAR-GROUP/BlazeIterative.git && \
cd BlazeIterative && \
cmake . && \
make install && \
cd .. && \
rm -rf BlazeIterative
git clone https://github.com/nonlocalmodels/NLMech.git
cd NLmech
mkdir build
cd build
cmake .. -DHPX_IGNORE_COMPILER_COMPATIBILITY=ON -DCMAKE_BUILD_TYPE=Release -DEnable_Tools=ON
make -j 2
I am very sorry, but I do not have the capacity, to submit the missing packages to Ubuntu or Debian. I maintain the Blaze and HPX on Fedora, which is time-consuming.
@Kevin-Mattheus-Moerman We agree that the installation is not quite straight forward, as @chennachaos mentioned that many of the libraries are not available as system packages yet.
However, we do not have the capacity to add these packages as system packages or to spack, since it is so difficult to get funding for open source software.
@chennachaos could you reply to @diehlpk 's comments? :point_up: thanks.
Sorry, I didn't notice that @diehlpk already responded.
Although, all the instructions seem to be available for Fedora, not everyone uses Fedora. However, installation on different architectures is only minor issues for this library. I believe that @diehlpk will help resolve the installation issues if the users struggle to install the library on other systems.
At this point, I recommend NLMech library for publication in JOSS.
Thanks @chennachaos. Would you be able to tick the boxes at the top if you are happy to recommend acceptance?
Thanks @chennachaos. Would you be able to tick the boxes at the top if you are happy to recommend acceptance?
Done!
@whedon generate pdf from branch joss
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@diehlpk I have now read your paper in detail. Below are some minor comments/suggestions on the paper. Feel free to disagree with some of these:
...the two regime of deformation...
peridynamic
be written as peridynamics
? I see several of your references do this. Neighborhood of point...
-> The neighborhood of point...
...is typically taken as the ball...
one would say ...is typically defined as all points contained in the sphere...
pariwise force
-> pairwise force
In the library...
, I recommend referring to NLMech again since it is a while at that point since you did, just to make it clear e.g. In the NLMech library...
For example, regarding input files for these models, we refer to the collection of examples in the documentation.
perhaps something like: Sample input files for these types of models are provided as examples in the documentation.
As a side note this seems to be the first mention of "input files", without having seem the documentation/software the reader is not aware that NLMech requires input files. If the examples and documentation are complete (e.g. they include a description of the use of input files) perhaps you could rephrase this further as:Examples for these types of model implementations are provided in the documentation.
...of arbitrary domain...
this should probably read ...of an arbitrary domain...
or ...of arbitrary domains...
...neighboring points in ball...
be rewritten as ...neighboring points in the ball...
(although I would suggest using sphere instead. ...either central difference or...
, would this be better ...either a central difference or...
or ...either the central difference or...
Once you have worked through the above, please do the following
@whedon generate pdf
v0.1.0-rc1
) should be updated?@whedon check references from branch joss
Attempting to check references... from custom branch joss
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/17m1112236 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.1007/s10659-018-9672-7 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.2172/1226115 is OK
- 10.1016/j.cpc.2008.06.011 is OK
- 10.1016/j.ijimpeng.2016.09.003 is OK
- 10.1016/j.camwa.2017.06.045 is OK
- 10.18419/opus-2879 is OK
- 10.1007/978-3-319-06898-5_5 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-015-9564-z is OK
- 10.1016/j.compstruc.2004.11.026 is OK
- 10.1007/978-3-319-22977-5_33-1 is OK
- 10.21105/joss.02352 is OK
- 10.1109/hpcsim.2012.6266939 is OK
- 10.1007/s42102-018-0004-x is OK
- 10.1007/s42452-020-03784-x is OK
- 10.6084/m9.figshare.12320726.v1 is OK
MISSING DOIs
- 10.31224/osf.io/gty2b may be a valid DOI for title: A comparative review of peridynamics and phase-field models for engineering fracture mechanics
INVALID DOIs
- None
@whedon check references from branch joss
Attempting to check references... from custom branch joss
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/17m1112236 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.1007/s10659-018-9672-7 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.2172/1226115 is OK
- 10.1016/j.cpc.2008.06.011 is OK
- 10.1016/j.ijimpeng.2016.09.003 is OK
- 10.1016/j.camwa.2017.06.045 is OK
- 10.18419/opus-2879 is OK
- 10.1007/978-3-319-06898-5_5 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-015-9564-z is OK
- 10.1016/j.compstruc.2004.11.026 is OK
- 10.1007/978-3-319-22977-5_33-1 is OK
- 10.21105/joss.02352 is OK
- 10.1109/hpcsim.2012.6266939 is OK
- 10.1007/s42102-018-0004-x is OK
- 10.1007/s42452-020-03784-x is OK
- 10.6084/m9.figshare.12320726.v1 is OK
- 10.31224/osf.io/gty2b is OK
MISSING DOIs
- None
INVALID DOIs
- None
* Should `peridynamic` be written as `peridynamics`? I see several of your references do this.
@Kevin-Mattheus-Moerman Yes, several references doing this, however, I decided to use peridynamic and many other authors do this.
This is written on Wikipedia for the difference between peridynamic and peridyanmics.
The term "peridynamic," an adjective, was proposed in the year 2000 and comes from the prefix peri, which means all around, near, or surrounding; and the root dyna, which means force or power. The term "peridynamics," a noun, is a shortened form of the phrase peridynamic model of solid mechanics.
@whedon generate pdf from branch joss
Attempting PDF compilation from custom branch joss. Reticulating splines etc...
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references from branch joss
Attempting to check references... from custom branch joss
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/17m1112236 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.1007/s10659-018-9672-7 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.2172/1226115 is OK
- 10.1016/j.cpc.2008.06.011 is OK
- 10.1016/j.ijimpeng.2016.09.003 is OK
- 10.1016/j.camwa.2017.06.045 is OK
- 10.18419/opus-2879 is OK
- 10.1007/978-3-319-06898-5_5 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-015-9564-z is OK
- 10.1016/j.compstruc.2004.11.026 is OK
- 10.1007/978-3-319-22977-5_33-1 is OK
- 10.21105/joss.02352 is OK
- 10.1109/hpcsim.2012.6266939 is OK
- 10.1007/s42102-018-0004-x is OK
- 10.1007/s42452-020-03784-x is OK
- 10.6084/m9.figshare.12320726.v1 is OK
- 10.31224/osf.io/gty2b is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon check references from branch joss
Attempting to check references... from custom branch joss
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/17m1112236 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.1007/s10659-018-9672-7 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.2172/1226115 is OK
- 10.1016/j.cpc.2008.06.011 is OK
- 10.1016/j.ijimpeng.2016.09.003 is OK
- 10.1016/j.camwa.2017.06.045 is OK
- 10.18419/opus-2879 is OK
- 10.1007/978-3-319-06898-5_5 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-015-9564-z is OK
- 10.1016/j.compstruc.2004.11.026 is OK
- 10.1007/978-3-319-22977-5_33-1 is OK
- 10.21105/joss.02352 is OK
- 10.1109/hpcsim.2012.6266939 is OK
- 10.1007/s42102-018-0004-x is OK
- 10.1007/s42452-020-03784-x is OK
- 10.6084/m9.figshare.12320726.v1 is OK
- 10.31224/osf.io/gty2b is OK
MISSING DOIs
- None
INVALID DOIs
- None
Your paper is about to be accepted in JOSS, we recommend you proofread the paper once more yourself
@Kevin-Mattheus-Moerman I asked some native speaker to read the paper one more time.
I will prepare the final release today and upload the paper to FigShare after my meeting marathon.
@whedon check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1137/17m1112236 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cma.2019.03.024 is OK
- 10.1007/s42102-019-00010-0 is OK
- 10.1007/s10659-018-9672-7 is OK
- 10.1007/s10704-020-00480-0 is OK
- 10.2172/1226115 is OK
- 10.1016/j.cpc.2008.06.011 is OK
- 10.1016/j.ijimpeng.2016.09.003 is OK
- 10.1016/j.camwa.2017.06.045 is OK
- 10.18419/opus-2879 is OK
- 10.1007/978-3-319-06898-5_5 is OK
- 10.1007/s10659-007-9125-1 is OK
- 10.1007/s10659-013-9463-0 is OK
- 10.1007/s10659-015-9564-z is OK
- 10.1016/j.compstruc.2004.11.026 is OK
- 10.1007/978-3-319-22977-5_33-1 is OK
- 10.21105/joss.02352 is OK
- 10.1109/hpcsim.2012.6266939 is OK
- 10.1007/s42102-018-0004-x is OK
- 10.1007/s42452-020-03784-x is OK
- 10.6084/m9.figshare.12320726.v1 is OK
- 10.31224/osf.io/gty2b is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: @diehlpk (Patrick Diehl) Repository: https://github.com/nonlocalmodels/NLMech Version: v0.1.0 Editor: @Kevin-Mattheus-Moerman Reviewer: @vijaysm, @chennachaos Archive: 10.6084/m9.figshare.16688695.v1
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
Status
Status badge code:
Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
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@vijaysm & @chennachaos, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Review checklist for @vijaysm
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @chennachaos
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper