Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @StewMH and @mdavezac, it looks like you're currently assigned as the reviewers for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

Attempting PDF compilation. Reticulating splines etc...

👉 Check article proof 📄 👈

👋 @StewMH, @mdavezac - thanks for agreeing to review this submission. Your job, as stated in the first comment in this issue, is to go through the paper and the software repository, and check off the boxes in your list as you've done so. When you find something that is a problem, if it's brief, you can mention it here, and if it's less brief or an action for the submitter, open an issue in the software repository and mention this issue in it.

If you have any questions or problems, please tell me.

Hi @tesch1,

I tried compiling this with GCC 7.3 and got this error:

In file included from /home/smh/joss/cppduals/duals/dual_eigen:389:0,
                 from /home/smh/joss/cppduals/tests/sandbox.cpp:20:
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h: In function ‘Packet Eigen::internal::pset1(const typename Eigen::internal::unpacket_traits<Packet>::type&) [with Packet = Eigen::internal::Packet2cdf; typename Eigen::internal::unpacket_traits<Packet>::type = std::complex<duals::dual<float> >]’:
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h:157:21: error: ‘_mm256_set_m128’ was not declared in this scope
   return Packet2cdf(_mm256_set_m128(v,v));
                     ^~~~~~~~~~~~~~~
/home/smh/joss/cppduals/duals/arch/AVX/ComplexDual.h:157:21: note: suggested alternative: ‘_mm256_set_epi8’
   return Packet2cdf(_mm256_set_m128(v,v));
                     ^~~~~~~~~~~~~~~
                     _mm256_set_epi8

I think you need a workaround here. See e.g. opencv/opencv#8080 for a similar issue.

I didn't have any luck compiling it with Clang on Ubuntu either, so far.

Also, it's Apache-licensed but you have MPL-licensed files:
https://gitlab.com/tesch1/cppduals/blob/master/duals/arch/AVX/Dual.h

Hi,

Thanks for reviewing!

Ah yeah, the "older gcc missing avx primitive". Just checked in an update/workaround. Does it compile for you now?

Also, did you run into the same error(s) under clang, or was there something else?

Regarding the licenses, yes, there are some files that were modified from Eigen, so retain the Eigen license. These are only included with #include <duals/dual_eigen>. An upcoming update will clarify this in the README.

@tesch1, have you considered dual licensing the non-eigen parts with MPL as well as Apache? That way, users can pick a format where the whole product is covered under a single license.

Oh yes, that's a great idea. I'll do that. I picked Apache+LLVM because libc++ uses it, and wanted to be broadly compatible with that, but dual-licensing is even better.

👋 Any news on this from the authors or reviewers?

Hi,

I have got past the missing avx primitive with GCC. Now the compilation runs for a while but fails with an ICE probably related to out-of-memory, at least on my VM. I can try a more powerful bare-metal machine, the VM only has 2G of RAM.

Cheers,
Stewart

An issue has been filed in the original repo.

@StewMH, I think I clicked on your checkboxes rather than mine at some point... I tried to undo the damage, but I do apologized if I made a mess of things 😊

@tesch1 - please let us know when you have worked on the issues in https://gitlab.com/tesch1/cppduals/issues/4

@whedon remind @tesch1 in 2 weeks

Reminder set for @tesch1 in 2 weeks

👋 @tesch1, please update us on how things are progressing here.

👋 @tesch1, please update us on how things are progressing here.

@whedon generate pdf from branch paper-3

@StewMH - did you ever get it to compile? Some Eigen constructs can be quite demanding on compiler memory, especially in newer (> 3.3.7) versions.

I've updated https://gitlab.com/tesch1/cppduals/issues/4 and merged changes into the master branch (which is currently building).

Regarding licensing, have changed everything to MPL-2 for simplicity's sake.

Attempting PDF compilation from custom branch paper-3
. Reticulating splines etc...

👉 Check article proof 📄 👈

@danielskatz It would appear that whedon does not correctly use custom branches from gitlab when generating pdfs (or I did the syntax wrong above?)

What didn't work? It looks like whedon generated a PDF. Is it not from the right branch?

It is not from the right branch.

👋 @arfon - can you help on this

What branch were you expecting changes from?

@whedon generate pdf from branch paper-3

Attempting PDF compilation from custom branch paper-3. Reticulating splines etc...

👉 Check article proof 📄 👈

so... it works when you do it, or it was queued up somewhere and didn't complete / wasn't available until sometime after whedon posted 'Check article proof' I'm quite certain that the link above (after I sent the whedon command) had the wrong version.

every once in a while, my safari seems to get confused and delivers a cached version...

but glad it's ok now.

Can you let us know where you think things are in terms of addressing comments from the reviewers?

I've updated https://gitlab.com/tesch1/cppduals/issues/4 and merged changes into the master branch (which is currently building).

👋 @tesch1 - are you ready for reviewers to look at this again?

👋 @StewMH, @mdavezac - please take a look at this and see if your concerns have been sufficiently addressed

👋 @StewMH, @mdavezac - pinging again...

Sorry, let me address this today

Hi @tesch1

How do I build and test the package? It's a while since I looked at this, and I'm now getting some weird errors if I try to build the tests:

cd cppduals/build
cmake ../tests/
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /cvmfs/sft.cern.ch/lcg/releases/gcc/8.3.0-cebb0/x86_64-centos7/bin/gcc
-- Check for working C compiler: /cvmfs/sft.cern.ch/lcg/releases/gcc/8.3.0-cebb0/x86_64-centos7/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /cvmfs/sft.cern.ch/lcg/releases/gcc/8.3.0-cebb0/x86_64-centos7/bin/g++
-- Check for working CXX compiler: /cvmfs/sft.cern.ch/lcg/releases/gcc/8.3.0-cebb0/x86_64-centos7/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
CMake Warning (dev) at External_GTest.cmake:17 (set):
  Cannot set "GTEST_INCLUDE_DIRS": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:16 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at External_GTest.cmake:18 (set):
  Cannot set "GMOCK_INCLUDE_DIRS": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:16 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at External_GTest.cmake:31 (set):
  Cannot set "GTEST_LIBRARY": current scope has no parent.
Call Stack (most recent call first):
  CMakeLists.txt:16 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Error at CMakeLists.txt:21 (include_directories):
  include_directories given empty-string as include directory.


CMake Error at CMakeLists.txt:24 (include_directories):
  include_directories given empty-string as include directory.

Hi @StewMH - the tests directory is a dependent subdirectory of the base - so you need cmake .. instead of cmake ../tests. But also cmake flags to enable testing/benchmarking, from the base cppduals dir: (I'll update this in the docs too)

cd cppduals/
cmake -Bbuildx -H. -DCPPDUALS_EIGEN_LATEST=OFF -DCPPDUALS_TESTING=ON -DCPPDUALS_BENCHMARK=ON
cmake --build buildx --target all
cmake --build buildx --target test

Disclosure: I cant test this at the moment, because I just got a new machine and the latest Apple clang is crashing on building the tests, but it should work. Gah.

Edit: ON not OFF

OK, on Red Hat I have this issue:

-- Looking for sgemm_
-- Looking for sgemm_ - not found
CMake Error at /cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase/x86_64/Cmake/3.14.3/Linux-x86_64/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find BLAS (missing: BLAS_LIBRARIES)
Call Stack (most recent call first):
  /cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase/x86_64/Cmake/3.14.3/Linux-x86_64/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  /cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase/x86_64/Cmake/3.14.3/Linux-x86_64/share/cmake-3.14/Modules/FindBLAS.cmake:766 (find_package_handle_standard_args)
  tests/CMakeLists.txt:98 (find_package)

But I do have a BLAS:

/usr/lib/libblas.so

👋 @StewMH - note that @tesch1 is trying to help with your issue, but needs your feedback to proceed.