Hi, I am having a fatal problem installing yt on my MacBook Pro running OS X v10.9.4. I am using the install script, with the options set as follows: # Here's where you put the HDF5 path if you like; otherwise it'll download it # and install it on its own #HDF5_DIR=/opt/local/lib # If you need to supply arguments to the NumPy or SciPy build, supply them here # This one turns on gfortran manually: #NUMPY_ARGS="--fcompiler=gnu95" # If you absolutely can't get the fortran to work, try this: #NUMPY_ARGS="--fcompiler=fake" INST_HG=0 # Install Mercurial or not? If hg is not already # installed, yt cannot be installed. INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with # the system zlib, which is compiled statically. # If need be, you can turn this off. INST_BZLIB=1 # On some systems, libbzip2 is missing. This can # lead to broken mercurial installations. INST_PNG=1 # Install a local libpng? Same things apply as with zlib. INST_FTYPE=1 # Install FreeType2 locally? INST_ENZO=0 # Clone a copy of Enzo? INST_SQLITE3=1 # Install a local version of SQLite3? INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a # working TeX installation. INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? INST_ROCKSTAR=1 # Install the Rockstar halo finder? INST_SCIPY=0 # Install scipy? After downloading and activating Xcode command line tools, I got the script to complete successfully. I activated it using the activate.csh script. However, when I then try to start yt, it pauses for 30 seconds or so, and then issues the response “Abort”, with no further errors. I get the same response if I try to import yt into the python (running in the yt environment). Abort, and return to the command line. I have tried erasing the yt-x86_64 directory and reinstalling from scratch, with no change in behavior. I also examined the yt_install.log. I found a number of, presumably irrelevant, errors in the configuration tests, but also an error at the end of the long section on building Ipython (almost at the end of the script, just before readline assembly that looks possibly relevant: gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.3.0 Thread model: posix clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' make[1]: *** [libreadline.6.2.dylib] Error 1 make: [shared] Error 2 (ignored) Any insight on how to proceed? Best, Mordecai -- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
just "abort" usually tells me it can't find enough memory while loading the executable. I assume you got plenty of that. On linux I would then use 'strace' to see if the kernel tells me more. And the ldd command to see what shared libs it might need. On a mac, there appears to be the dtruss command for strace. Me and Mac appear to be in a continues state of dislike, all I got was dtrace: failed to initialize dtrace: DTrace requires additional privileges so I'm sure somebody can tell me what that means (I don't have admin on that mac) peter On 09/28/2014 03:36 PM, Mordecai-Mark Mac Low wrote:
Hi, I am having a fatal problem installing yt on my MacBook Pro running OS X v10.9.4. I am using the install script, with the options set as follows:
# Here's where you put the HDF5 path if you like; otherwise it'll download it # and install it on its own #HDF5_DIR=/opt/local/lib
# If you need to supply arguments to the NumPy or SciPy build, supply them here # This one turns on gfortran manually: #NUMPY_ARGS="--fcompiler=gnu95" # If you absolutely can't get the fortran to work, try this: #NUMPY_ARGS="--fcompiler=fake"
INST_HG=0 # Install Mercurial or not? If hg is not already # installed, yt cannot be installed. INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with # the system zlib, which is compiled statically. # If need be, you can turn this off. INST_BZLIB=1 # On some systems, libbzip2 is missing. This can # lead to broken mercurial installations. INST_PNG=1 # Install a local libpng? Same things apply as with zlib. INST_FTYPE=1 # Install FreeType2 locally? INST_ENZO=0 # Clone a copy of Enzo? INST_SQLITE3=1 # Install a local version of SQLite3? INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a # working TeX installation. INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? INST_ROCKSTAR=1 # Install the Rockstar halo finder? INST_SCIPY=0 # Install scipy?
After downloading and activating Xcode command line tools, I got the script to complete successfully. I activated it using the activate.csh script.
However, when I then try to start yt, it pauses for 30 seconds or so, and then issues the response “Abort”, with no further errors. I get the same response if I try to import yt into the python (running in the yt environment). Abort, and return to the command line.
I have tried erasing the yt-x86_64 directory and reinstalling from scratch, with no change in behavior. I also examined the yt_install.log. I found a number of, presumably irrelevant, errors in the configuration tests, but also an error at the end of the long section on building Ipython (almost at the end of the script, just before readline assembly that looks possibly relevant:
gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.3.0 Thread model: posix clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' make[1]: *** [libreadline.6.2.dylib] Error 1 make: [shared] Error 2 (ignored)
Any insight on how to proceed?
Best,
Mordecai
-- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Mordecai, We've had some reports about incompatibilities with the install script on OS X Mavericks recently, but I don't think this error has been reported before. Unfortunately getting the install script to work portably in all cases is a labor of love and sometimes errors like these crop up. Googling for your error returns this discussion on the readline mailing list: https://lists.gnu.org/archive/html/bug-readline/2013-12/msg00002.html. Apparently the version you're compiling needs to be patched to compile cleanly on mavericks. I haven't checked whether the patch has made its way into a readline release. I'm not sure what exactly is compiling readline (IPython maybe?), but earlier in the install script we should have installed a pure-python version of the readline library from pypi if we were unable to import it. It would help to figure out what went wrong if you could upload the full install log somewhere. Do you have a python environment setup on your laptop already? It's very straightforward to install yt using anaconda, canopy, or a manually configured python environment, bypassing all the bootstrapping that the install script must do. Take a look at the following page in the documentation: http://yt-project.org/doc/installing.html#installing-yt-using-anaconda http://yt-project.org/doc/installing.html#installing-yt-using-pip-or-from-so... Hope that's helpful. -Nathan On Sun, Sep 28, 2014 at 12:36 PM, Mordecai-Mark Mac Low <mordecai@amnh.org> wrote:
Hi, I am having a fatal problem installing yt on my MacBook Pro running OS X v10.9.4. I am using the install script, with the options set as follows:
# Here's where you put the HDF5 path if you like; otherwise it'll download it # and install it on its own #HDF5_DIR=/opt/local/lib
# If you need to supply arguments to the NumPy or SciPy build, supply them here # This one turns on gfortran manually: #NUMPY_ARGS="--fcompiler=gnu95" # If you absolutely can't get the fortran to work, try this: #NUMPY_ARGS="--fcompiler=fake"
INST_HG=0 # Install Mercurial or not? If hg is not already # installed, yt cannot be installed. INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with # the system zlib, which is compiled statically. # If need be, you can turn this off. INST_BZLIB=1 # On some systems, libbzip2 is missing. This can # lead to broken mercurial installations. INST_PNG=1 # Install a local libpng? Same things apply as with zlib. INST_FTYPE=1 # Install FreeType2 locally? INST_ENZO=0 # Clone a copy of Enzo? INST_SQLITE3=1 # Install a local version of SQLite3? INST_PYX=1 # Install PyX? Sometimes PyX can be problematic without a # working TeX installation. INST_0MQ=1 # Install 0mq (for IPython) and affiliated bindings? INST_ROCKSTAR=1 # Install the Rockstar halo finder? INST_SCIPY=0 # Install scipy?
After downloading and activating Xcode command line tools, I got the script to complete successfully. I activated it using the activate.csh script.
However, when I then try to start yt, it pauses for 30 seconds or so, and then issues the response “Abort”, with no further errors. I get the same response if I try to import yt into the python (running in the yt environment). Abort, and return to the command line.
I have tried erasing the yt-x86_64 directory and reinstalling from scratch, with no change in behavior. I also examined the yt_install.log. I found a number of, presumably irrelevant, errors in the configuration tests, but also an error at the end of the long section on building Ipython (almost at the end of the script, just before readline assembly that looks possibly relevant:
gcc -dynamic -arch i386 -arch x86_64 -arch_only `/usr/bin/arch` -install_name /usr/local/lib/libreadline.6.2.dylib -current_version 6.2 -compatibility_version 6 -v -o libreadline.6.2.dylib readline.so vi_mode.so funmap.so keymaps.so parens.so search.so rltty.so complete.so bind.so isearch.so display.so signals.so util.so kill.so undo.so macro.so input.so callback.so terminal.so text.so nls.so misc.so xmalloc.so xfree.so history.so histexpand.so histfile.so histsearch.so shell.so mbutil.so tilde.so compat.so -lncurses Apple LLVM version 6.0 (clang-600.0.51) (based on LLVM 3.5svn) Target: x86_64-apple-darwin13.3.0 Thread model: posix clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' clang: error: invalid argument '-compatibility_version 6' only allowed with '-dynamiclib' make[1]: *** [libreadline.6.2.dylib] Error 1 make: [shared] Error 2 (ignored)
Any insight on how to proceed?
Best,
Mordecai
-- Mordecai-Mark Mac Low Curator & Professor +1-212-496-3443 Department of Astrophysics +1-212-769-5007 (fax) American Museum of Natural History mmaclow (Skype, Hangout) 79th St at CPW, NY, NY, 10024-5192, USA
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
-
Mordecai-Mark Mac Low -
Nathan Goldbaum -
Peter Teuben