[yt-users] Trouble Installing Yt with Rockstar

Nathan Goldbaum nathan12343 at gmail.com
Tue Nov 28 19:34:17 PST 2017


Sorry, typo, that should read “fork”, not “form” (stupid autocorrect).

On Tue, Nov 28, 2017 at 10:33 PM Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> 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.
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>
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