several errors in compiling/installing

[albemengoni]

hi, i get 3 warnings and 2 errors while i do:

make -j4 install

can you help?

error output enclosed.

thanks, a mengoni

[Jonas Lippuner]

What compiler are you using? Can you please do "rm -rf *" in the build directory and then run CMake again and send me the output of CMake?

[albemengoni]

compiler is gcc7. i just sent in the CMakeOutput.log by gmail.

[albemengoni]

here is the CMakeOutput.log thanks, am

[Jonas Lippuner]

Uhm, where did you sent the output to? I didn't get anything

[albemengoni]

i just replied to an email which i got with my first comment.

[albemengoni]

i cannot attach files with these comments...

[albemengoni]

ok. here it is again...

[Jonas Lippuner]

Thanks, I got your email, but it is not exactly what I need. I need the console output you get when you run CMake. So please do the following:

$ cd /Users/alberto/cernbox/research/SkyNet/jlippuner-skynet/build_dir
$ rm -rf *
$ cmake -DSKYNET_MATRIX_SOLVER=<what you used before> -DCMAKE_INSTALL_PREFIX=<what you used before> ..

And then upload the console output to this issue. You can upload additional files by clicking on the Edit button for this issue.

[albemengoni]

ok. it is in the attachment list.

[Jonas Lippuner]

Aha, you're using AppleClang, not GCC. I have never tested SkyNet with AppleClang, so please use GCC by doing the following:

$ CXX=g++ CC=gcc FC=gfortran cmake <rest as before>

Also, if you want to run a network with more than 100 species or so, you cannot use Armadillo. It's dense solver and it will be way too slow to run a big network. If you don't have access to Intel MKL, I recommend you use Pardiso (see the INSTALL file for info on where to get it).

Finally, are you doing this on Mac OS? If so, be warned that I don't test SkyNet on Mac and a lot of people had issues getting it to work on Mac (most issues were in connection with HDF5), although it is possible. If you can, it may be easier to run SkyNet on Linux.

[albemengoni]

thanks. but still not working. 47% built, but two errors appear. meanwhile, i installed the MKL libs. - out_config - out_install enclosed.

[Jonas Lippuner]

Ah, I think that's a Mac issue. Please comment out lines 14, 15, and 21 in src/Utilities/FloatingPointExceptions.cpp.

[albemengoni]

OK, that's solved. however, I run into the HDF5 issue that you mentioned. i enclose again the out_install for your reference. it looks like there are problems with other libs as well (boost and gsl). thanks anyway.

[Jonas Lippuner]

Unfortunately, I don't have access to a Mac computer and so I can't test SkyNet on Mac. It looks like you don't have the right libraries (HDF5, boost, MKL, GSL) since it says that it can't find the symbols for architecture x86_64. Since I don't currently support Mac for SkyNet, I would recommend you install and run SkyNet on a Linux machine. If that is not possible, then you could try to compile your own versions of HDF5, Boost, and GSL, and use Pardiso instead of MKL. Make sure you compile those libraries with GCC and not the default Mac compiler. You could then use CMAKE_PREFIX_PATH to point CMake to your versions of these libraries and it might work. I can't promise that it'll work, though. Sorry.

[Jonas Lippuner]

Compiling SkyNet on Mac OS is currently not officially supported. It may be supported in the future