Error installing dealii by candi on Apple M1

[Masoud Ahmadi]

Hi,

I am trying to install dealii on a apple ARM M1 OSX, using the following instructor:

https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX

However, I get the following error:

error: use of undeclared identifier 'H5Pset_dxpl_mpio'
  status   = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);
             ^
/Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:3242:63: warning: unused parameter 'filename' [-Wunused-parameter]
ScaLAPACKMatrix<NumberType>::load_parallel(const std::string &filename)
                                                              ^
/Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20: error: use of undeclared identifier 'H5Pset_fapl_mpio'
  status         = H5Pset_fapl_mpio(plist_id, tmp.grid->mpi_communicator, info);
                   ^
/Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:10:16: note: in instantiation of member function 'dealii::ScaLAPACKMatrix<double>::save_parallel' requested here
template class ScaLAPACKMatrix< double >;
               ^
/Users/masoud/dealii-candi/tmp/unpack/deal.II-v9.3.3/source/lac/scalapack.cc:2861:20: error: use of undeclared identifier 'H5Pset_fapl_mpio'
  status         = H5Pset_fapl_mpio(plist_id, tmp.grid->mpi_communicator, info);
                   ^
/Users/masoud/dealii-candi/tmp/build/deal.II-v9.3.3/source/lac/scalapack.inst:20:16: note: in instantiation of member function 'dealii::ScaLAPACKMatrix<float>::save_parallel' requested here
template class ScaLAPACKMatrix< float >;
               ^
1 warning and 3 errors generated.

[Timo Heister]

Did you make any changes to candi.cfg? Can you also please post how you execute candi.sh (what arguments)?

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[Masoud Ahmadi]

Dear Timo,

No, I did not change anything; I did exactly what is explained in the following link, step by step:

https://github.com/dealii/dealii/wiki/Apple-ARM-M1-OSX

[Timo Heister]

What candi git branch are you on? You might need to switch to master to make things work for now.

Can you post how you execute candi.sh including the first few pages of output?

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/957d0cc5-e3a8-4922-a770-794a3192a6a0n%40googlegroups.com.

[Masoud Ahmadi]

Thanks Timo,

I tried to switch to master, but again the same thing happened. 

So, now on the master branch of candi, same error.

I attached the log file, please take a look.

[Timo Heister]

Can you please post your /Users/masoud/dealii-candi/tmp/build/deal.II-master/detailed.log ?

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6fcaf535-65c6-4d28-84ef-ccabd4e12833n%40googlegroups.com.

--

Timo Heister
http://www.math.clemson.edu/~heister/

[Masoud Ahmadi]

I had removed candi, so I had to reinstall it.

But again got the same error.

The requested log file is attached. Please see.

[Timo Heister]

> # SCALAPACK_LIBRARIES = /opt/homebrew/lib/libscalapack.dylib;-lm;-

It looks like you have a scalapack installation that got picked up and
caused the error. Can you do
cmake -D DEAL_II_WITH_SCALAPACK=OFF .
in the directory where you found the detailed.log? Follow that by
make install
(you can use -j to use more cores of course).

> To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/e4821e6f-0b25-43f5-8353-6d8903b523b0n%40googlegroups.com.

[Masoud Ahmadi]

Thanks Timo.

I removed homebrew entirely, then reinstall it and just run:

brew install cmake open-mpi gcc

Then I install the master version, this time the setup was completed; however, when I tried to run step-1 example, this happened:

[Masoud Ahmadi]

I removed this Master version, and install 9.3.3 version, it worked!
Many thanks Timo.

[Hemiao Zhang]

Hi! I am also trying to install Dealii on Apple M1 Monterey 12.2.1. I also got similar "failure with exit status: 2". May I ask what is the difference between the master version in this conversation and v9.3.3? Many thanks in advance.

[Fred RIchards]

I also have the same issue, irrespective of whether I try to compile using the v9.3.3 or the master version of deal.ii. I'm on Apple M1 Monterey 12.3.

Here's the compilation error for source/base/hdf5.cc:

In file included from /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/source/base/hdf5.cc:20:

/Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1470:30: error: use of undeclared identifier 'H5Pset_dxpl_mpio'

          const herr_t ret = H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);

                             ^

/Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1502:21: error: use of undeclared identifier 'H5Pget_mpio_actual_io_mode'

              ret = H5Pget_mpio_actual_io_mode(plist, &io_mode);

                    ^

/Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/include/deal.II/base/hdf5.h:1505:17: error: use of undeclared identifier 'H5Pget_mpio_no_collective_cause'

                H5Pget_mpio_no_collective_cause(plist,

                ^

3 errors generated.

Seems odd as the correct version of hdf5 and all associated libraries seems to be found OK in the configuration step.

[Timo Heister]

Can you post the output of "grep HDF5 detailed.log" in the directory /Users/fr714/dealii-candi-basic/tmp/unpack/deal.II-v9.3.3/ please?

[Fred RIchards]

Hi Timo,

The output I get is:

#        DEAL_II_WITH_HDF5 set up with external dependencies

#            HDF5_DIR = /Users/fr714/dealii-candi-basic/hdf5-1.10.7

#            HDF5_INCLUDE_DIRS = /Users/fr714/dealii-candi-basic/hdf5-1.10.7/include

#            HDF5_USER_INCLUDE_DIRS = /Users/fr714/dealii-candi-basic/hdf5-1.10.7/include

#            HDF5_LIBRARIES = /Users/fr714/dealii-candi-basic/hdf5-1.10.7/lib/libhdf5_hl.dylib;/Users/fr714/dealii-candi-basic/hdf5-1.10.7/lib/libhdf5.dylib

Best,

Fred