Just a comment:

Using the full path to the compilers (e.g. using /usr/bin/gcc instead of gcc) will fail because of a sed command (line 329 in install_script.sh) using the forward slash as a separator. If the compilers are in your bath, you might want to specify them directly by name, rather than the full pathname.

The install script should probably be changed to use something other than forward slash as the delimiter, at least in this case where it might get mangled with pathnames. Something like changing

... -e "s/CC=gcc/CC=${CC}/ ...

to

... -e "s|CC=gcc|CC=${CC}| ...

Chris

On Tue, May 21, 2013 at 7:58 AM, Britton Smith brittonsmith@gmail.comwrote:

Hi Paul,

Welcome to yt!

We have had a number of problems in the past using gnu compilers that are not the ones installed with xcode. I recommend you try again with those compilers. To do that, you should be able to just do: export CC=/usr/bin/gcc export CXX=/usr/bin/g++

Please, let us know if that doesn't work. Also, if it doesn't, please just send us the last 10 or 20 lines of the output log from the install script. That should be enough to diagnose the problem.

Britton

On Tue, May 21, 2013 at 10:19 AM, Paul La Plante plaplant@andrew.cmu.eduwrote:

...

Hi,

I am having trouble installing yt on my personal machine using the install script. I downloaded the script from the suggested website ( http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh) and attempted to execute it with `bash install_script.sh.' I have tried a few different combinations of install options, but it always seems to fail while building matplotlib. My system is OS X 10.8.3, and gcc version 4.8.0 (installed from MacPorts). I have attached my yt_install.log.

Thanks in advance for any help!

Best regards, Paul

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Hi Paul,

This is due to an issue that has been fixed in the latest development version of yt.

Can you try installing that instead? The development install script is here:

http://hg.yt-project.org/yt/raw/yt/doc/install_script.sh

-Nathan

On May 21, 2013, at 10:07 AM, Paul La Plante plaplant@andrew.cmu.edu wrote:

Thanks for your assistance. As Britton suggested, I used the Apple-provided compilers. But as Chris noted, I had trouble with sed while trying to export CC, so I made a symbolic link instead (to llvm-gcc, I'm not sure if it matters). Now it crashes on the 'Installing yt' step. The error message is included below. It looks like it can't link against gomp.

I am currently running again using Apple-provided non-llvm gcc to see if this fixes the problem.

-Paul

---

    FAILURE REPORT:

---

ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) error: Command "/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -mmacosx-version-min=10.7 build/temp.macosx-10.4-x86_64-2.7/yt/utilities/lib/geometry_utils.o -lm -o yt/utilities/lib/geometry_utils.so -fopenmp" failed with exit status 1

---

---

On May 21, 2013, at 12:57 PM, Chris Malone chris.m.malone@gmail.com wrote:

...

Just a comment:

Using the full path to the compilers (e.g. using /usr/bin/gcc instead of gcc) will fail because of a sed command (line 329 in install_script.sh) using the forward slash as a separator. If the compilers are in your bath, you might want to specify them directly by name, rather than the full pathname.

The install script should probably be changed to use something other than forward slash as the delimiter, at least in this case where it might get mangled with pathnames. Something like changing

... -e "s/CC=gcc/CC=${CC}/ ...

to

... -e "s|CC=gcc|CC=${CC}| ...

Chris

On Tue, May 21, 2013 at 7:58 AM, Britton Smith brittonsmith@gmail.com wrote: Hi Paul,

Welcome to yt!

We have had a number of problems in the past using gnu compilers that are not the ones installed with xcode. I recommend you try again with those compilers. To do that, you should be able to just do: export CC=/usr/bin/gcc export CXX=/usr/bin/g++

Please, let us know if that doesn't work. Also, if it doesn't, please just send us the last 10 or 20 lines of the output log from the install script. That should be enough to diagnose the problem.

Britton

On Tue, May 21, 2013 at 10:19 AM, Paul La Plante plaplant@andrew.cmu.edu wrote: Hi,

I am having trouble installing yt on my personal machine using the install script. I downloaded the script from the suggested website (http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh) and attempted to execute it with `bash install_script.sh.' I have tried a few different combinations of install options, but it always seems to fail while building matplotlib. My system is OS X 10.8.3, and gcc version 4.8.0 (installed from MacPorts). I have attached my yt_install.log.

Thanks in advance for any help!

Best regards, Paul

---

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---

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---

yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

---

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For others listening in, this fix will be included in the next stable release in ~10 days.

On Tue, May 21, 2013 at 12:37 PM, Paul La Plante plaplant@andrew.cmu.eduwrote:

Hi Nathan,

Thanks for the tip! Switching to the developer version fixed this.

-Paul

On May 21, 2013, at 1:10 PM, Nathan Goldbaum nathan12343@gmail.com wrote:

Hi Paul,

This is due to an issue that has been fixed in the latest development version of yt.

Can you try installing that instead? The development install script is here:

http://hg.yt-project.org/yt/raw/yt/doc/install_script.sh

-Nathan

On May 21, 2013, at 10:07 AM, Paul La Plante plaplant@andrew.cmu.edu wrote:

Thanks for your assistance. As Britton suggested, I used the Apple-provided compilers. But as Chris noted, I had trouble with sed while trying to export CC, so I made a symbolic link instead (to llvm-gcc, I'm not sure if it matters). Now it crashes on the 'Installing yt' step. The error message is included below. It looks like it can't link against gomp.

I am currently running again using Apple-provided non-llvm gcc to see if this fixes the problem.

-Paul

---

    FAILURE REPORT:

---

ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: warning: directory not found for option '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/' ld: library not found for -lgomp clang: error: linker command failed with exit code 1 (use -v to see invocation) error: Command "/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/ -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/ -mmacosx-version-min=10.7 build/temp.macosx-10.4-x86_64-2.7/yt/utilities/lib/geometry_utils.o -lm -o yt/utilities/lib/geometry_utils.so -fopenmp" failed with exit status 1

---

---

On May 21, 2013, at 12:57 PM, Chris Malone chris.m.malone@gmail.com wrote:

Just a comment:

Using the full path to the compilers (e.g. using /usr/bin/gcc instead of gcc) will fail because of a sed command (line 329 in install_script.sh) using the forward slash as a separator. If the compilers are in your bath, you might want to specify them directly by name, rather than the full pathname.

The install script should probably be changed to use something other than forward slash as the delimiter, at least in this case where it might get mangled with pathnames. Something like changing

... -e "s/CC=gcc/CC=${CC}/ ...

to

... -e "s|CC=gcc|CC=${CC}| ...

Chris

On Tue, May 21, 2013 at 7:58 AM, Britton Smith brittonsmith@gmail.comwrote:

...

Hi Paul,

Welcome to yt!

We have had a number of problems in the past using gnu compilers that are not the ones installed with xcode. I recommend you try again with those compilers. To do that, you should be able to just do: export CC=/usr/bin/gcc export CXX=/usr/bin/g++

Please, let us know if that doesn't work. Also, if it doesn't, please just send us the last 10 or 20 lines of the output log from the install script. That should be enough to diagnose the problem.

Britton

On Tue, May 21, 2013 at 10:19 AM, Paul La Plante <plaplant@andrew.cmu.edu

...

wrote:

...

Hi,

I am having trouble installing yt on my personal machine using the install script. I downloaded the script from the suggested website ( http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh) and attempted to execute it with `bash install_script.sh.' I have tried a few different combinations of install options, but it always seems to fail while building matplotlib. My system is OS X 10.8.3, and gcc version 4.8.0 (installed from MacPorts). I have attached my yt_install.log.

Thanks in advance for any help!

Best regards, Paul

---

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---

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