[yt-users] Trouble Installing Yt with Rockstar

[Nathan Goldbaum]

Hi Sean,

This is a known issue and fixing it will require a fix in our form of
rockstsar. I’m personally unsure how to fix it. See
https://github.com/yt-project/yt/issues/1289

If you have any idea how to modify rockstar to fix this that would be very
much appreciated.

If you build on Linux you will likely not hit this issue.

Nathan

On Tue, Nov 28, 2017 at 8:49 PM Sean Larkin <sflarkin at ucsc.edu> wrote:

> I have been trying to install Rockstar with yt onto a computer running
> macOS sierra 10.12, using both the install script and manually.
>
> For the install script, I get this error:
>
> Building Rockstar
>
> ********************************************
>
>         FAILURE REPORT:
>
> ********************************************
>
>
>     config=config)
>
>   File
> "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/build.py",
> line 1147, in build
>
>     utils.check_call_env(cmd, env=env, cwd=src_dir)
>
>   File
> "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py",
> line 628, in check_call_env
>
>     return _func_defaulting_env_to_os_environ(subprocess.check_call,
> *popenargs, **kwargs)
>
>   File
> "/Users/user1/Rockstar/yt-conda/lib/python3.6/site-packages/conda_build/utils.py",
> line 624, in _func_defaulting_env_to_os_environ
>
>     return func(_args, **kwargs)
>
>   File "/Users/user1/Rockstar/yt-conda/lib/python3.6/subprocess.py", line
> 291, in check_call
>
>     raise CalledProcessError(retcode, cmd)
>
> subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e',
> '/Users/user1/Rockstar/yt-conda/conda-bld/rockstar_1511919771484/work/conda_build.sh']'
> returned non-zero exit status 2.
>
>
> ********************************************
>
> ********************************************
>
> Failure.  Check /Users/user1/Rockstar/yt-conda/yt_install.log.  The last
> 10 lines are above.
>
>
>
>
>
> And when installing manually, after stating "make lib" i get this error:
>
> /bin/sh: pkg-config: command not found
>
> gcc -m64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64
> -D_BSD_SOURCE -D_POSIX_SOURCE -D_POSIX_C_SOURCE=200809L -D_SVID_SOURCE
> -D_DARWIN_C_SOURCE -Wall -fno-math-errno -fPIC  -shared rockstar.c
> check_syscalls.c fof.c groupies.c subhalo_metric.c potential.c nfw.c
> jacobi.c fun_times.c interleaving.c universe_time.c hubble.c integrate.c
> distance.c config_vars.c config.c bounds.c inthash.c io/read_config.c
> client.c server.c merger.c inet/socket.c inet/rsocket.c inet/address.c
> io/meta_io.c io/io_internal.c io/io_ascii.c io/stringparse.c io/io_gadget.c
> io/io_generic.c io/io_art.c io/io_tipsy.c io/io_bgc2.c io/io_util.c
> io/io_arepo.c io/io_hdf5.c -o librockstar.so -lm -O3 -std=c99
>
> In file included from server.c:241:
>
> *./load_balance.c:8:21: **warning: **using floating point absolute value
> function*
>
> *      'fabs' when argument is of integer type [-Wabsolute-value]*
>
>       i = ceil(sqrt(fabs(in)))+1;
>
> *                    ^*
>
> *./load_balance.c:8:21: **note: *use function 'llabs' instead
>
>       i = ceil(sqrt(fabs(in)))+1;
>
> *                    ^~~~*
>
>                     llabs
>
> 1 warning generated.
>
> Undefined symbols for architecture x86_64:
>
>   "_GROUPIES_fast3tree_box_inside_sphere", referenced from:
>
>       _GROUPIES_fast3tree_find_sphere_offset in groupies-eb1fe8.o
>
> ld: symbol(s) not found for architecture x86_64
>
> clang: *error: *linker command failed with exit code 1 (use -v to see
> invocation)
>
> make: *** [lib] Error 1
>
> I am not sure what is causing the error for install script, but for the
> manual install, I think it is clang using the wrong c++ standard library. I
> have attempted to change the library used, but nothing has worked for me so
> far.
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